I have a functioning 3D ragdoll in a Godot 4.0 project but not totally sure how the collision masks are intended to be setup. The only documentation I've found so far is https://docs.godotengine.org/en/stable/tutorials/physics/ragdoll_system.html, which seems pretty out of date and missing a ton of information, seems to indicate that the PhysicalBone3Ds should be on their own collision layer with nothing selected for a mask and the map StaticBody3Ds should have their masks set to the PhysicalBone3D's collision layer. This doesn't appear to work, I had to flip it and set the bones to mask out the map collision layer, which is whatever, just odd that the article had it backwards. The second issue is that if I have it setup like this, the bones aren't colliding against themselves so I get limbs sticking through the torso, etc. This seems wrong, but if I have the bones mask themselves then I get a ton of jitter and the bones never fall asleep.
Does anyone know what the intended setup is? The jitter is so bad that makes me think the article is right but that would mean that the ragdolls wouldn't be able to interact with multiple instances of themselves, which kinda defeats the purpose? At this point I'm assuming I'm missing a field that needs to be adjusted to get rid of the jitter and weird physics.
(FYI, for those who are trying to get ragdolls working and are having a hard time finding information. This is the only resource I've found that bothers to explain how the constaint guides work.
Also, make sure your armature/bones has a scale of 1 otherwise when you turn on the bone physics they will snap to the armature scaling and do terrible things. My models/rig are from mixamo which came with a 0.001 scale by default, unfortunately applying the scale in Blender completely jacks up all of the mixamo animations. My solution was to set the scale on the armature to 1 (in the object properties, do not apply scale) then use the "Root Scale" slider in the *.blend file import settings. Even after all of this Godot still throws scaling warnings on the physical bones that it auto-generated for me. I couldn't get them to go away, I tried removing all scaling keyframes from the animations and manually editing the TSCN file to set all of the bone scales to 1, none if got rid of the warnings. I ended up ignoring them since I wasn't seeing any strange behavior.)