Yes. Every operator works on non-humanoid rigs except for the Bone Hierarchy Fixer, which is built specifically around Unity's Humanoid bone requirements. Enabling it on a non-humanoid rig will either fail (if required humanoid bones are missing) or reorder the hierarchy in ways you may not want. Everything else, generation, normalization, retargeting, baking, works regardless of rig type.

Yes. Only the Bone Hierarchy Fixer is written for Unity's Humanoid system specifically, and you're not required to use it. The hierarchy the Bone Hierarchy Fixer creates is solid in general, even outside Unity.

Yes. You can have multiple Animation Rig/Game Rig pairs in the file, and any Animation Rig can have multiple Game Rigs, though the latter has little use since it's not recommended to adjust Game Rigs after generation (e.g. to create variants) unless you're sure you won't be updating the rig anymore.

The intended workflow is to export the finalized Game Rig as FBX first, then convert to VRM/VRChat format as a separate step. Adding special properties directly to Game Rig bones goes against the intended workflow, since updating the Game Rig will overwrite them.

It's not recommended, but you can. Any edits you make will be overwritten the next time you update the Game Rig.

Yes. Since Game Rig meshes are duplicates of your Animation Rig meshes, shapekeys carry over automatically (meshes aren't stripped the way bones are).

The addon itself isn't tied to a specific export format. FBX is recommended because it's a safe default that most game engines accept, including Actions/animations. Whether a given format works for you comes down to whether it supports what you need.

No. The addon duplicates the Animation Rig and does all its work on that duplicate (the Game Rig). Your Animation Rig is never touched, unless you select it and run "Update Game Rig" (which is only intended to be used on Game Rigs), or when you manually select it as a Game Rig target inside the Manual Operators panel. Even then, every operation is a standard Blender operator, so Ctrl+Z works normally.

Yes. Bone naming convention only matters when using the Bone Hierarchy Fixer operator, which allows you to input your own bone names in the panel. You can also create your own persistent bone mapping preset by duplicating the Default.json file in the bone mapping preset folder and editing it in a text editor.