Good ideas, however I am not entirely sure what we can achieve without the source code. That being said, there are ways to edit the masks (for body, underbelly etc.) so that we can include color changes for the pawpads, mouth areas, and inner ears. The only problem that will arise will be the lack of creativity. You won't be able to edit the colors individually.
For example: In Kov's game before FeralHeart, Impressive Title, when you changed one of the eyelid colors, it also changed the color of the tongue as well. That would be the only issue that (I can think of) would limit the creativity. Though, if you wouldn't mind that then I suppose it's not that much of a problem.
Most of these edits sound like they could just be add-ons, since I am sure there would be some users that wouldn't like these changes. So, I cannot really see it being implemented into a public patch. I wouldn't mind, since I have had the idea of editing the masks as such myself.
You can surely add markings to the paw pads, but it wouldn't be it's own separate thing. Pretty sure it would be a body marking, if anything. These sort of things are easily achieved with a preset, so it would purely be to add to the default look to those who cannot view your preset. Same with the fur textures, their main reason is to up the realism of FeralHeart and personal presets. Perhaps there would be someone kind enough to compile a package of free fur textures, so that one could have many of them to their disposal at once. Same for the animations.
I have had many of these ideas myself, so I see no problems for me personally. Though, it would be difficult without the source code to add most of those features. However, I do not know what all we are able to do without the source code. Some of these are individual items, and more suitable for mods rather officially in the game.