I have been using emulators for almost 2 decades now, never seen one which can not go full screen ó_o
And in any case, a black border imo does nothing to break immersion in any way. You are looking at a picture on a rectangle in front of you, surrounded by room. I doubt that the rectangle having a bunch of black around the actual image changes anything for most people, but I grant you that you might be an exception. I for one prefer clean pixels and a slightly smaller viewing area over blurred and bigger.
VGA can be scaled nicely to 1600x1200 if you want clean, and even if you use a different scale you could do something like you are doing and scale so that it only needs to be applied vertically. 1024x768 is ancient by now, even my monitor from 1996 could run 1600x1200.
And small stuff like 100:94 scale pixels can be neglected. I agree that in some cases (like VGA even) it can look weird to have the wrong aspect, CPS stuff being a more extreme case than VGA for example. And for CPS you kinda need something like you are doing (Which newer versions of MAME do perfectly well for example), because the resolution required to scale cleanly without antialias between pixels is pretty huge.