It probably won't be that bad. It's true that Volkswagen uses a different process than the rest of the world. But communication "on a functional level" is possible, for example through the V2N connection also available at Volkswagen.
In addition, the specification of one or the other standard does not necessarily mean that the respective car manufacturer is included in his system. Corresponding control units from Tier One such as Bosch and Continental are able to support both standards. Onn Haran, CTO of the semiconductor supplier Autotalks, points out that it is also possible to adapt the vehicles to a changed standard via an OTA software update.
“Eventually, all markets will converge on a single technology, and the over-the-air flexibility would enable an OEM to switch during vehicle lifetime from one technology to the other, if the market converged to a different technology than predicted”, Haran explains. This aspect however gives the update capability of cars a new weight. For future vehicles, it will become indispensable.