Theres no reason not to have a water pump replaced under warranty, regardless of being tuned or stock.
There’s no scan required to diagnosis a leaking WP, thus it’s a non issue.
I personally haven’t had any water pump issues on my GTI (120,000 miles, owned since new) or my GLI (21,000 miles & owned since new), but I do know of dozens who’ve had the warranty work performed no questions asked on modded cars.
Idk what you guys think you’re saving by not having them fix this common issue for free, but TD1 would only apply to something like throwing a rod or melting a piston…your stage whatever tune doesn’t mean you can’t have them warranty interior rattles, crack sun roof, leaking water pump or anything else that has absolutely nothing to do with the tune.