If they choose they could attempt to look at bolts for scraches, or in the case of my shifter they can physically look at it an tell its about 2" or so shorter. I use quality parts and I understand basic auto mechanics. If something is outside my scope of ability a professional mechanic does it.
I am not attempting to "get one over" on the dealership. If I modify something and it breaks I have no problems replacing or repairing that. In the case of the 02-05 WRX where pieces of the cat can break off and harm the turbo and they tried to deny me based on a short shifter.. we would have some serious words.
If that same BOV causes the fuel pump to go bad (it is highly unlikely but can happen) then that would be my fault for adding a 50/50 bov that causes the car to use slightly more fuel between shifts. This is my fault and I'd have no problem fixing it.
Legally they cannot deny a warranty claim due to modifications unless they can prove that the modification directly related to the warranty claim in question. I have seen many dealerships attempt to "screw" people out of a warranty they rightfully paid for, such as denying claims because they added a K&N no replace air filter, painted the break callipars, or my personal favorite the carpet ripped and the "aftermarket" floormats were to blame not the fact that the carpet was installed improperly. (this was a suzuki dealership)
Warranty is not my primary concern, but as I said if I can keep it I will, if they say no more warranty then I'm not concernerned.