If it is too difficult to modify the GUI, it could rather be done via a file on the root file system, of the form
plugginName pre-gain post-gain
pluggin1 3 -3
pluggin2 6 -2
When we build the pedalboard on the UI, the GUI manager looks up the table and inserts (or not) the appropriate gain units in between the jack clients. The output gain and input gain of two consecutive boxes can be automatically combined in a single one.
Regarding latency, although it is a single multiplication per sample, at the jack level, it is performed using buffers, which means that one would have potentially up to roughly twice as much jack buffers being dealt with, right ?