Similar concept to the mk2, but you need to get an insert that exactly matches your mk3 mount that comes in two versions. On that criteria, I would suggest the Powerflex ones are the best bet with two shape versions to fit the two variants of the mount, and each available in four different hardnesses, from soft diesel (red), regular (yellow), track/high-power (purple) to race (black). So you can choose your compromise between comfort and performance. Reasonably priced and decent hardware. Still have to install mine though instead of the Neuspeed.
As for warranty, long term it is possible that you wear out the mount itself quicker because of friction with the insert (this is why a close fit is important), but that should be long past the warranty period. Can't see how they would object having it there otherwise. If anything, it should keep things from breaking...