Ok, I’m just starting out with Premiere, but I’ve found that it does NOT affect the final export–
I use proxies since my computer is so slow. The proxies I make are LOW res (180)… and when I import them onto my 1080p timeline (24p DSLR)… they are tiny. I right-click each clip, “Scale to Frame Size” and they fill up my preview window, as expected.
Upon final export – I “replace footage” with all my original HD files… and the final MP4 (for YouTube) looks exactly like what I edited.
Took me a little while to figure that out… but, it’s simple. Hopefully that helps!