So, the answer to most of your question are kind of linked to each other, even though you made it 3 different questions.
So your goal essentially is to be able to share animations and be able to tweak animations, while also doing as little full animating as possible. You want to mix and match across lots of places, and use root motion.
Cool cool. So, with Godot's retargeting, you can mix and match animations from Mixamo, from Rigodotify, from Stinty, from really anywhere that uses a standard skeleton that you can map into Godot. You can bring in as many animations as you like, save them into libraries, and share them across all your models. So whether to use Rigodotify, Mixamo, or some other skeleton as your base, depends on your needs.
If you just want to reuse animations, just rig a model in Mixamo, map it into Godot. You're done.
If you want create your own animations and have more control. Use Rigodotify for convenient control Rig, make the animations in there, you can always add Mixamo animations to it as libraries later in Godot. If you want some premade libraries, i have a few hundred animatins on my github i give away, some aren't great, but still, it's a massive free library so, have at it: https://github.com/catprisbrey/Godot4-OpenAnimationLibraries
Root bone should be on the floor, yes. And it should animate any velocity movement you want in your game. So forward and backward for walking, left and right for strafing. Etc etc. If a mixamo one is flying all over, it's probably thinking the hips are the root or something, and that's not what you want. Root is generally pretty steady. Some mixamo animations i believe are setup for root, they'll have a checkbox "in place" or not, and you want to have it NOT be in place, so that root drives it forward.
If you need videos on retargeting, and using libarries, my youtube channel is full of them. You'll probably want these ones relating to animation here:
https://youtube.com/playlist?list=PL35yqmsJzxjvuYNgoxrxpOFxu5ZzwhbZ5&si=4WrdbQAo...
I cover a lot on animation retargeting, using libaries, making your own, etc. Hope this answers your questions, and gives you places to find answers.