I'm using 3/4" on 11/16th" wood and there's no way I would attempt to trim it down. I doubt I could get a straight cut, and it would show. The whole point of t-molding is to hide the imperfections of the wood edges.
Regarding does it really look bad to have a bit of overlap? No. Doesn't look bad at all. But if I need to open my control panel, it rubs against the overlap (over time wears it down. makes it all ratty looking). Same goes if I need to pull the speaker panel out.