Please help Recall Electic Water pump

I took 2008 to dealer for recall repair work and estimate on headlamp repair.
Mechanic says rubber edge guard over tire needs to be cut or removed to access both electric water pump being upgraded based on recall. I was called to discuss and come see the guard they say was installed after market. They have to cut or remove but did not mention replacing.
My question is, shouldn't Toyota be responsible for edge guard replacement? I paid for many upgrades which were on the car when I purchased it brand new, hardly any miles on it.

Also they pointed out small amount of pink spray on hood and in engine, said I need regular water pump removed. Cost is 408 dollars, way too much money.