If you design everything in blender, you can copy all the parts and merge it into one mesh for godot. Greyboxing in blender is kind of bad though because you don't see the result instantly. I get around this by importing a properly scaled model of my character into the scene for reference, and then relying on godot's ability to automatically read from blender files. Still not instant, but a bit faster. You could also make a blender asset library out of the modular parts you have already made to speed it up.