Greetings, Timothy Lanfear and Peter Gentry -
I'm afraid I do not have a solution to your problem(s), but I do have some input. I'm a violist who plays fiddle tunes and classical music. I also transpose a lot of fiddle tunes to play on the viola. I agree that it's a lot easier for me to proofread in the original clef, and I sometimes forget to change clefs after proofreading. However, I think there would be problems with doing an automatic clef change with transposition, at least in classical music. Viola uses both alto and treble clef, and cello uses bass and tenor. I suspect other instruments use multiple clefs (and ottava), as well. You would still have to check and change the results of your transposition, and I, personally, think I have a better chance of doing that consistently if I have to do it all the time.
Just my 2 cents,
Ralph Palmer