it would be very useful to be able to transpose and tune an instrument rather than its individual samples.
For transposing I see 2 ways of doing that:
1) transposing the mapping
2) transposing the samples
For tuning, I think the only way is to change the base frequency of the samples. If several instruments are mapping to the same sample I suppose the user should be informed of it and ask whether to proceed or not.
The way I imagine that is when right-clicking on the "Sample Map" box (under the instrument tab) additional items appear on the pop-up menu to transpose +/- 1, and fine tune (say +/-1/32, that is 1 of 32th semi-tone, or any another appropriate granularity).
openMPT is terrific