i recently had my transmission nearly completely replaced but when i got the car back i noticed they didn't place back on the rubber boot that sits underneath the leather.

anyone have an idea if that piece actually helps with shifting?

 

I've fixed your topic title to be more descriptive.

"is there any difference..., better/worse..or no difference at all."

Doesn't say anything about your question.

The inner boot is supposed to be there, to seal h20 and dirt from the passenger compartment. It has nothing to do with how the trans shifts.