There are only 2 ways to address the problem with an ECU remap:
Depending on the ECU hardware it may be possible to have switchable maps and the car switched back to stock prior to a dealer visit. I know that APR offer this for some models. Of course this only avoids a tech discovering the tune from a test drive. If the tech uses a scanner on the ECU the reflash can be detected.
Flash back to stock map. But as above a tech can still scan the ECU and see that it has been flashed, however since the map is stock then the car has not been modified, as per terms of warranty.
The "piggyback" tuning box avoids this issue because they are easy to remove leaving no evidence, however there genuinely are two other issues:
It is not possible to achieve the same level of performance as with a proper ECU remap.
Related to this they can be crude and as such "possibly" detrimental to long-term reliability. For example if they only fool the ECU by interposing in pressure measurement without any affect on fuelling, relying on the ECU to detect lean and make its own adjustments then the ECU will be operating outside the range qualified by the OEM. If the OEM has a very rigorous design and testing system then this might be OK, but if not then the engine might still run a bit lean, and that is bad, especially for turbo cars.
FYI I have never had any issue with dealers and my tuned cars. I am honest with them and they have been fair in return. This has included warranty work where the failure was unrelated to the engine.