This is patently false. If you let 100 minutes go by, the visible timer simply freezes at 99:59.99, but you can continue to play. In SADX, that's all there is to say about it, but in the original Dreamcast version, the timer continues ticking invisibly, all the way up to 127:59.99 until it too stops with no consequence. That extra time is never fully visible anywhere, but parts of it can be gleamed from the level complete screen, or from the trial mode level selection screen if for some reason that 100+ minute completion happens to be your best time.
SA2 doesn't have anything version-specific there, just a cap at 99:59 and you can continue on your merry way, having lost all semblance of a time bonus more than an hour and a half ago.
But there are some things it does have version-specific, and the reason I came to post here is one of them.
This is what happens when you fill out abandoned object entries with null bytes instead of deleting them entirely. 131 of them all in the same file...quite a collection of discarded data for the team that ported and revamped the levels.