I believe, if you want to conform to fluff, you plain can't apply genetic modifications to an already infected individual.
HMHVV is a magical disease that will keep the infected just the way the virus is programmed to like it, including making you immune to mind-altering nanites and he like. If your GM wants to allow that, I'd suggest a Delta-Clinic.
Genetic modifications are based on modified HMHVV after all, and I reckon the original has something to say about that. ^^
Other than that, I believe things like bio-compatibility are about the body being more accepting of foreign things being introduced, where as genetics in all forms just change the base.
I would argue it would make sense for "Transhuman Prototype" to also allow genware in that one point of free essence, where by RAW it doesn't, but other than that I believe genetics to be entirely seperate, in the same way that injected hard nanites are probably the epitome of cyberware, yet they aren't.