I'm not aware of such plugin, but you could write one for yourself: just render to
ViewportTexture, frame by frame, then combine them in a spritesheet. And yes, transparent background is possible.
In Godot and in general. Is it better to use sprites or motion calculations?
It depends on hardware. A lot of animated objects are eating CPU, while large spritesheets are
consuming a VRAM.
Aside from that, not knowing actual task, hardware specs, all this looks like "premature optimization", and should be avoided at initial stages. The power of node-structured engines (and Godot in particular) is a decoupling: you can swap render technique anytime, without rewriting application-logic parts. Do this when you're close to final.