[sciurius]

- transpose e.g. to D, 2 semitones up from C, save changes
- the song is displayed in B (3 semitones down from D), correct

Well, it is equally valid to say that this is not correct.
You transposed the song display from C to A.
After changing the source from C to D, the song should still be displayed in A.

This is where key transposition bites interval transposition.

Did you transpose the display to A? Then it should still display in A (fixed key).
Did you transpose the display up 3 semitones? Then it should display in B (fixed transposition).

For example, what I often do: If I have a song in C, transpose the display to A and when the song is settled (rehearsed, ready to be performed) I change the song source to A (and cancel the transposition) since that's how is it going to used.

Having said all that, I personally have no problem with the current (fixed transposition) behaviour.