This is an oddity, although it might be Tails at fault. According to the style guides, Amy should be exactly in the middle of Sonic and Tails, and with the old sprites... ...she is. In motion however, Tails has the bigger head, arms and feet. Both characters are technically off-model (though to be fair, the "model" didn't exist for either when these sprites were drawn), with limbs presumably exaggerated because there weren't many pixels to play with. Because these two never appeared on screen together, you wouldn't notice the hacks. The mistake in Origins Plus is that Amy is designed to look like her Sonic CD sprite and/or the style guides. In reality, neither will do, because Tails is following a different set of rules. Her features need to grow a bit and her animations, have to become more exaggerated... which puts her at odds with what she looked like in Sonic CD. In short, they followed the rules, but the rules are wrong.