Yep, that's the problem. It is compounded if you have an Intro of say four bars and then a section A in the same key, and then a section B in a different key. The key signature in the transposed version is then only correct for the first four bars.
I hear what you say but I think it is rather an obvious thing to have been overlooked. I was thinking more that the limit of what you can do with the existing code has been reached. Believe you me, working with a software company myself, I can appreciate the problem. And software development takes soooo long these days. It is not like the old DOS days at all.

But I hope you are correct and I am wrong.