So, I think I'm seeing the confusion here. Doing as you said there makes the ragdoll into an animated prop which must be posed using the advanced bone tool or joint tool. This makes sense if you are using it specifically as an animated prop to pose with tools, not the physgun, hence why you have no issues with it. The issue with the knees and fingers are present in the base model which I have to assume is the reason that you don't see anything wrong with it as you are working with the animated prop variation. Correct me if this is wrong, but I think this may be the root of the problem lol.

Spawn the model.
Select the "animated prop tool" and then "alt-fire" with it on the model.
Spawn it again (always with the tool just mentioned) and you'll have the ragdoll ready to be posed.

The knees bend to the side instead of backwards, something I’d consider broken, but there’s clearly a solution since you have no problem with it. That being said, I assume that means I’m doing wrong with the tools, hence why I’m asking how to fix it with the tools.

I've no problems with them, so why should I fix something that isn't even broken...?

So, if you're not going to fix the joints, can you explain how you use the tools to fix them?

PLEASE FIND OUT HOW TO I NEED IT A NPC PLEASE

No idea how to do that

i beg to god make it a npc please

Again..I don't have such problems. Neither with the tools, I got problems or such

??? its literally the most obvious and simple thing to fix, the fingers roll left and right instead of bending down and up when using the finger poser

I don't have those problems

finger posing is incorrect, rotates instead of bending, ive noticed it on most of your models mind fixing it?

@Anita Radcliffe you deadass murdered the poor guy! stop he's already dead!

@Anita Radcliffe LMAO

He wears a paper bag to hide his ugly face