Can't imagine it would be a problem. I've taken my car in with exhaust and they just say "car sounds great" and this is from a dealership that has told me they advise against even doing a simple vagcom mod.
Ultimately if something breaks down because of what you did then I would expect them to not cover the repair. No way you're getting TD1 flagged for it though because they won't even know it's there when performing simple service. These guys shortcut their jobs just like everyone else; rarely will they do more than what's expected of them.
Blow a turbo? I'd get them off as soon as possible just because they're connected to the turbo (not because it was necessarily the reason).
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