Hi Alistair,
To do that, you'd need to create a variation of the set item and then edit that variation and adjust the capo number. Either edit the set item in the main set list and set it to a variation, or using the transpose pop-up, leave the transpose slider untouched and click the 'Variation' option. You can then edit the variation.
Unfortunately sets only contain a 'preferred key' for the song, not how a transpose should happen. If the song is in a different key in the set, the app creates a temporary variation behind the scenes and does a simple transpose on the entire song (the capo fret is left as it is).
I will, however, try to add the transpose by capo change if you try to transpose a variation for the next release (if it is possible!).