However, my biggest gripe is that there's no way - unless someone can tell me how - that you can start a sequence and leave it running, then when needed just press another key and it transposes it. If one uses hold, then you just layer the transposed sequence.
I may be misunderstanding your question, but I would use a hold
pedal. You keep the pedal down and just lift it briefly after hitting the new key. The layering only lasts for the brief moment between the keypress and pedal lift. (My first instrument was piano, so this is a pretty fundamental, automatic technique to me.)
One other possibility is to use the hold button in combination with unison, and set unison key mode (in misc params) to Last Note (or Last Retrigger). Unison mode will disable the layering and the key mode will give priority to the most recent keypress.