It is actually a feature
You made a good point. I try to explain.
When RC works with chords, it refers to chord notes by their index (root/first=0, second note=1, third note=2...etc). I used to display this differently in the past, like Ch#1, Ch#2, Ch#3 but that was also cryptic. Because the second note is typically the 3rd, and the third note is usually the 5th, I decided to show "3rd" for the second chord note, and "5th" for the 3rd chord note, even though this is misleading. E.g. because of this, the middle note of sus2 is still labelled as "3rd", and the 3rd note in a diminished chord is labelled as "5th".
Some operations like editing voicing create a new chord internally, but this messes up the order of chord notes, so the new bottom note becomes the root/first, etc. The phrases do not access the original chord, think of it as a pipeline when everything is transformed from one form to the other.
In the phrase editor it is important to know which notes are chord relative notes, but in the composition I don't think it matters how an original chord note was transformed and rendered to get the final MIDI note. In the future 'chord variations' will be added to the master track which will make this even more complicated.
I do not know yet how to fix this, but some kind of mapping from the original chord notes would be needed. Probably I will remove this display option entirely because it makes more problems than it solves. Thanks for bringing this up!
When transposing a phrase using the 'Phrase' transpose option to preserve the shape, in this case the chord notes are transposed, so the indexes are rearranged, like when voicing is edited.
I am sorry for the confusion.