This is how I have worked with scores. All parts written in main key then use transpose in \bookpart output section. This allows midi output for all parts in same key for audio review and PDF output for instrumentalists in proper key for their instrument. If you use variables for your parts (e.g., "trumpet= {}" then you can use "\transpose d c { trumpet }" where you have the variable used for its part).
I've written a few arrangement leadsheets, and being able to use transpose like this on performer request is, well, brilliant. A few edits, re-engrave, all done.