well, this would give you more of a reason to mod your car now!
they can't void any other parts besides the strict engine parts, so I would go have fun and do some turbo/manifolds/etc... mods.
if you think about it this way, it was going to happen sooner than later if you really plan to mod the sucker. it sucks that the guy seems to be a bit misleading when it comes to allowing modded cars.
he seems to be a bit sleezy in saying "no problem, bring it in" and then turn around and blacklist the car. this is a big warning sign with two cars from the same SA. sounds like a backstabber.
There are plenty of SA's that would continue to work on the car, and then give notification that for a particular problem with a vehicle, mods directly related will cause issues with warranty.
my old SA from my modded m3 was awsome. i came in with the car freshly dropped. he looked at it, and said "you know, you may have some issues with warranty with that car". I asked like what, and he said "you know, your shocks and springs" I'm like no sh*t. No problem replacing wheel bearings, TA bushings, diff, half shafts, checking for subframe.
I would check recommendations from others here regarding SA's in your area before servicing a car, modded or stock.