I assume you do a LOT of IFR
The problem is that if you want to do any overt IFR then you need a plane with an ICAO CofA, and an IR which matches the registration.
By "overt IFR" I mean IFR departures and IFR arrivals. In practice anybody can fly (illegally) enroute in IMC, and I am sure many Permit pilots do just that.
Also, the practical advantage of being able to go fully IFR (airways) is that you can climb on top of the muck and sit there in sunshine, and lack of turbulence.
That is why people pay so much money. If nobody wanted this capability, the world would be taken over totally by non-CofA planes flying (cough cough) "VFR".
There is also a distinct shortage of non-CofA 4-seat tourers that can carry 2 or 3 people, and more than a toothbrush, a decent distance. I fly a TB20 and even if I could only go VFR I would still keep it as long as I can.
I don't want to digress into yet another CofA v. Permit debate but you did ask the question about IFR.
Back to avionics, a lot of avionics get "sorted" unofficially. Lots of people have nice collections of installation manuals (which, while not being confidential, are restricted in availability) and sort out their own issues. It's generally untraceable because no inspector can ever tell if such and such a wire was installed by who, 10 years ago. Avionics also get reconfigured by users, to enable additional features.