[itsme]

* is not supported by MSP and by no other app that I came across so far

Text in square brackets is commonly used as a workaround for text that is intended to be shown above the lyrics.
[Astronomical/C] is a pretty theoretical example but [D.C. al Fine], [Break] or [Coda] might be in practical use and are not wanted to be transposed.

I know of at least two cases where note names in lowercase should be transposed:
1.) In very traditional folk music or in classical music, sometimes minor chords are written in lowercase [cm] at least in Germany. This looks a bit outdated for me and might be irrelevant for MSP or ChordPro, but who knows...
2.) It is common to use lowercase characters for a few single notes to notate small intros or fills. It is pretty confusing if they are not transposed. The reference implementation allows lowercase when      
"notenames" : true,
is set.
MSP doesn't support that by now

There are more possible improvements for MSP's ChordPro implementation. Maybe Mike could think about a ChordPro rework after finishing the current big tasks MSP for iPad and song versioning.