Yup, that's exactly what I'm seeing. Between the low source texture resolution and the posterization created by the low color depth, original textures often have these large monocolored blocky regions. As tempting as it is to just soften the source and use it as a background to the high-res texture to preserve the original tint, I've found out the hard way that it's almost never that simple. You instead end up with what we have here-- the original texture visible as a blurry thumbprint on the new texture.
Only to a point. There are many textures in SS2 that are duplicated across families, that are clearly intended to be exactly the same surface, yet they have slight color differences due to being palettized to different master palettes. This problem is exacerbated in TDP, where every texture in the entire game is represented by a single 256-color palette. Of course some weird color shifts snuck in. I don't consider eliminating them to be a flaw.