It's actually Sky Sanctuary where the music playlist starts to go wrong IIRC - it doesn't have two slots allocated, with either DEZ1 or DEZ2 getting an extra slot it shouldn't have. But it's still there in the right order otherwise. If your question is really about how much of the rest of the game was already planned, this is the strongest evidence that pretty much all of it was, and since the level order, sound test and playlist all match each other in very nearly exact game order, the vast majority of the game's progression seems to have been planned from a very early stage and barely altered during development (compare to the internal zone order in S1 and S2).
Where does the level order differ? Flying Battery is the one everyone knows, which was fairly obviously designed to sit between Carnival Night and Icecap (the idea that both it and Icecap were meant to appear later in the game seems come from some overly generous implication). The other named zone is Hidden Palace, which doesn't seem to have been planned at all, as evidenced by being the only distinct act in the game not to have its own music (even as "Sky Sanctuary act 1" in the 3C protos there was music reuse afoot, suggesting to me that the concept wasn't even planned, let alone the name). Its level slot is $1601, at the back end of the list, beyond the main single player levels, competition levels and bonus stages. The other levels surrounding it are the LRZ/DEZ boss acts, which were probably not planned as far as being separate levels at least, and the "fake" HPZ you go to from a flashing ring to choose a special stage, so you can probably be confident that none of these ideas were well developed by the time S3 was finalised, if they had been considered at all.
But in terms of whether a "complete" S3 would have ended at Launch Base, I think it really depends what you mean by "complete". The whole thing as conceived would not have ended with Launch Base (nor Sandopolis) but it also seems highly likely that Launch Base was always going to be the split point once a split was confirmed - there's plenty of remnants of FBZ as something that should have happened before Launch Base, but very little suggesting anything afterwards was meant to be in the first half. All you really have is the level select, and given its general brokenness, Sonic 2 icons, immediate enablement of debug, almost impossible cheat and the availability of a level select on a complete save anyway, I doubt much effort had really gone into making it ready for public consumption. That's just my conjecture, really, but it fits - Launch Base is a very logical point to split the story and gameplay, and splits the zone numbers more or less evenly.
Just for the sake of it, some other leftovers that haven't been mentioned in the topic or have only been tangentially referenced: Flying Battery has a save icon that differs from S3&Ks, which also shows a different palette that we turned into an actual level palette in Sonic 3 Complete. I'm not aware of any genuine FBZ palette data still being present in S3, so I don't know if this is still how things would have been when S3 was released or if it's an artifact of something much earlier like the background in the HCZ save icon. The S3 save data format still recognises zone $04 as FBZ, in contrast to S3&K where the save data is reshuffled into gameplay order; the level picker on a clear save skips over $04, but you can happily create a savegame at zone $04 and get as far as seeing FBZ's title card before everything locks up. That savegame can quite reasonably be a Knuckles save too, giving you the well-documented behaviour of Sonic with Knuckles' signposts, level clear text and so on.
Some of the boss behaviour for Knuckles' versions of the bosses is present but incomplete. At some point I posted a PAR code to enable it, but I don't have it to hand. Off the top of my head, it's AIZ1, HCZ2 and LBZ2 that have been done. HCZ2 is correct; AIZ1 is almost correct, apart from fired bombs hanging around after the boss dies and turning into monitor graphics. LBZ2 is the interesting one - in a complete reversal of S3&K, Big Arm doesn't appear in Knuckles' version of events. When you defeat the laser boss, EggRobo flies upwards as in S3&K, but has some garbage graphics attached to the base of his machine, which seem to be his bomb. He then flies in from the left and drops it as in S3&K (no egg prison in between) except that it creates a single crappy explosion and nothing else happens.
On a more minor note, if you force yourself into Lava Reef's zone slot and watch a palette viewer, you can briefly see a lava palette start rotating before everything seizes up. This proves that at least some work was done on the other levels, though it may have been no more than that. Mushroom Valley has some object layout, too, but it's only springs/spikes/monitors, and they don't correspond to sensible positions on the final plane layout (I never bothered to check if they match the earlier MHZ layouts from the 3C protos, but it would be interesting to know). Other than that, there seems to be nothing of the other levels present, so while we can be pretty sure they were planned, we can't know what work was done on them, if any.
Some mechanical facts surrounding some of the observations here: in S3&K, the object layouts are always read from the S&K side, which is how the obvious HCZ/LBZ changes are implemented. There are small differences throughout all layouts, the most notable ones being that Knuckles' paths are in a highly variable state of completeness, with CNZ2 being the least and probably AIZ2 or LBZ2 being the most well polished. The exit to Knuckles' segment of LBZ2 flows way better in S3, by the way - it was probably changed so you couldn't outpace the rising water, but you can see that the plane layout was made for the original S3 flow. S&K's object list for Sonic 3 levels is wildly different from the original Sonic 3 object list, so you can't just point it at the other side of the ROM.
The whole of Mushroom Hill is always loaded whether you're playing S3&K or S&K, but the game sets a flag on startup to tell it which version is running, and this is checked in the level events code to seal off the first section, skip the flying/falling intros and start somewhere else (in a cutscene in Knuckles' case). The same flag is used for pretty much everything that should differ between the games, from locking the relevant zones/characters on the level select to stopping the giant rings from ever flashing. Loading up an S3&K level select savestate on S&K is probably the easiest way to bypass it and lets you get debug enabled too, but you'll have to be careful of going back to the title screen or trying to load one of the S3 zones, as they all fairly obviously depend on S3 data and will hang you up good.
Tails' sprites are indeed read from the S3 section apart from the additional sprites needed for S&K, which are stored separately. Interestingly, Sonic has a similar setup code-wise, retaining an identical copy of his Sonic 3 art in the S&K side and shifting to a different art offset for the extra poses (albeit one that sits immediately after his main sprites). Knuckles is not separated in the same way.
The FBZ boss coordinates are mildly interesting - act 1's boss is indeed in the exact position you'd expect to see it, but if you dump the S3 layout into S3&K, you'll hit act 2's boss too early, during the rising platform section. But if that platform never moved, and you judge the coordinates relative to the platform (which is pretty much how it works out anyway IIRC) the coordinates are indeed correct. S&K just doesn't have the boss in the object layout - the rising platform event spawns it once complete.
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(S&K Collection, Jam, Mega Collection, the Steam version, Generations and possibly more, all (at the very least) imply this to even someone who might not be familiar with Sonic 3.)
