I think it depends on the mods. And what the car is going in for. Mine went to Pierre on Lake City recenly for a rear end noise. I talked to the service manager about mods on cars under warranty. He said that as long as the aftermarket piece is not proven to be at fault for damage, that Ford would still warranty the car. They even install aftermarket parts on customers' cars under warranty. When mine was there there was an brand new 07 that the customer was having a CAI/Throttle body, and a full exhaust done on by the shop.
Ford of Kirkland is usually pretty cool about it. The service shop wanted to supercharge my cobra the day I bought it and they said they would waranty it, lol.