Depends on if your garage is mod-friendly. They could blame the fault on a non-oem part. Or they could politely overlook it. Or if you're RR, actively discuss modding with you!
....
That's right! I'm very lucky - Several of my VW dealership's mechanics are VW enthusiasts and also the Parts Manager. The guy in charge of the whole workshop worked for Ferrari for a number of years too.
To refuse a warranty claim they'd have to show that your aftermarket mod had played a
direct part in the issue. Regarding a filter I would have thought that could only be if your aftermarket filter failed to stop debris getting into the system and then caused a fault. You'd anyway then have recourse with the filter manufacturer. These things can get messy as each company would like to pass the buck but you have to think positive.
Choosing well proven aftermarket components makes a difference. When I asked my VW dealer their attitude if I remapped they asked who.. When I said I was considering Revo they said no problem. VW UK always have the final word on issues though (unless you take an issue to VW Germany).
Long story short: You'll be alright, Mandy
. HTH