Cypher2 is an analog modelling synth, so its V.C.A. is hard-wired to the output of the Amp Envelope to emulate the same function as any synth's final V.C.A. While this is unlikely to change, I'll happily pass on your suggestion to the development team.
Here's a link to an illustration showing how to assign the 5D TransMod source 'Press' to Vol in the Output Mixer section. This will enable you to use "pressure" or "aftertouch" to control the final output level (after the Effects stages), which may help.
Let us know if you have any other questions.
Is it possible to divorce the VCA from the amplitude envelope in a future release? I'm interested in using a Roli Seaboard MPE/5D parameter to exclusively control amplitude while the oscillator(s) drone.