Cheers! Issues 2 and 3 are likely due to the fact, that the build generated by setup.bat/.sh is a minimal editor buildmwith many modules disabled. I do this so iteratiom times on recompiles while working on the code are minimal. When we publish editor builds, they'll have all the default modules that come with Godot. You can fix this locally if you remove all lines from custom.py and recompile the engine/editor via setup.sh/.bat (build.sh/.bat will not work, as setup.sh/.bat configures the build).
Issue 1 is a documentation problem You don't want to create a track the SpineAnimatiomTrack in the animatiom editor, but the AnimationPlayer child of the track. Sadly, Godot's AnimationPlayer and editor don't allow custom track types, so this is a workaround. As a bonus you see the animation durations and names tho, which is MUCH better then only seeing a little diamond for a key.