I'm sure it was absolutely just a skill issue on my part. This was literally my first time trying to use that workflow (all of my other personal projects are still in the greybox phase) so I underestimated everything about it haha. I knew that working that way is fairly "industry standard" so I think I just assumed it would be as simple as just dropping the new asset in. The problem in Godot (at least as I was running into it) was that it was importing the object as an inherited scene. So it wasn't a simple process of editing the pieces of the model or its children pieces because I was innately locked out. And I couldn't figure out how to have this not happen on import nor could I find a simple way to just batch "clear inheritance" on the entire model. So that meant I couldn't create custom animations (at least not reasonably) because that would require manually going through the entire tree and finding the special place to "Make Unique" on every bone and limb that I'd want to manipulate. This just didn't feel worth it in the context of a jam (and luckily the model already had animations built in).
This was a bigger problem when replacing my placeholders for effects and in world UIs. Like using a cylinder as a placeholder for a laser is simple. But then when swapping that I had to completely change up my code to work in a different way. With a cylinder I could just stretch it simply along an axis to give it a "shooting" effect. I think the object I tried to swap it with was like a mushroom? And just stretching it along an axis wasn't working the same way for me.
All in all I'm sure there's a better and more correct way to do it. The real issue was that I left this for last when I only had like 6 or 7 hours until deadline. Once I started hitting issues I was torn between just trying to bruteforce things or taking the time to slowly learn an entirely new process. And doing anything slow at that point felt like the wrong choice. Especially when, at that point, I still had the starry eyed hope that I'd have time to add voice lines in!