Hobbiests are free to do a lot of things that manufacturers cannot do. I personally think this is a neat mod (but am not willing to up the retail price even more to include it for everyone whether they will use it or not). But, as a hobbiest, if you personally do this mod on your own scanner, you don't have to file for a permissive change with the FCC. You are, however, still held responsible if the mod causes interference and is found to be outside the limits for a Part 15 device or otherwise does not meet FCC rules for scanners (for example, if you figured out a way to modify the product to receive cellular and were caught, you could be at the receiving end of an FCC action)..
Actually, Jon is considered a manufacturer (in the eyes of the FCC) and his product is the combined scanner/GPS. He is responsible for FCC compliance and filing for a FCC grant for this modded product (but I seriously doubt that the FCC would care about such a small-scale and essentially hobbiest enterprise).
Technically, if the unit were to cause interference to other devices (I know this is an almost 0% probability for this mod), Jon could be on the hook for fixing the issue.
All that said, when it is sent to Uniden for repair, if there is evidence of the unit having been opened for any reason, the warranty is voided. This is true for every product we sell (and generally true for most electronic products anyone else sells). If there is no such evidence, then the warranty status would depend on the nature of the failure (just like any product from any other company).
If it comes in with the mod in place, the repair will be out of warranty, regardless of the nature of the repair, and we have to disconnect the mod. We have to do this because we are responsible for ensuring that the unit complies with the FCC grant and we can only do that by restoring the unit to factory condition. We can leave the mod physically in place (i.e. glued into the back cabinet), but when it is returned, it will be electrically disconnected from the scanner.
We can't be responsible for the GPS module itself. We wouldn't intentionally damage it, but if it were inadvertently damaged during repair, we would not be responsible for such damage (we likely would have no way to detect such damage in any event). So, the safest thing would be to have the mod carefully removed prior to sending it in for repair, then re-applied after it is returned from repair. This will not preserve the warranty (big hole in the back cabinet would be a pretty good clue that it had been opened), but it will ensure that all parts are returned in a usable state.