That is BS! The PKDM Civics screen is not connected with the OBD in the car, Nor does it operate the Air conditioning.
You can get a grip to grip audio system (no wiring cut) They cannot void your warranty. Usually people dont find a grip and get the wires cut (usual jugar cutting the wire and tieing them with tapes)
For example, If you get an after market audio and your cars suspension has a fault they cannot blame the audio system. But yes if their is a electronic fault due to the audio system, Your cars warranty is void.
How ever the pricing issue can be there, because from factory your OEM 2 Din audio system would be adjusted in the price of the NAV unit.