I would imagine the only issue would be if VW wanted more details on the actual car itself to dig a little deeper.
Yes, I'd have to agree with that. If your car displayed lots of signs of modifications that would sound warning bells to a technician and more importantly a warranty manager then you may run into issues if they dug deep into the car's brain to check for maps (which from my understanding isn't as involved as you may think as there are certain physical parameters that can be checked without fully examining the software, simple things like requested boost and injection/fueling/ignition).
I've had about ten remaps from various companies and have friends that have had maps from different ones again. There are only two mobile tuners that buy in their maps from overseas that I've encountered any problems with and they aren't active forum people on here.
I've never had any isses with taking a mapped VW/SEAT/Skoda in for servicing and have never had any warranty issues with an engine that even needed looking at.
Touch Wood!!!