I've welded stainless steel to mild steel loads of times on exhausts. No problem at all. They're just trying it on, either that or they're really that thick... in which case don't let then even look at your car! Just take your car anywhere that has a mig welder, it will take them 2 mins!
I think the Powerflow warranty only applies if you are the one who had it fitted. Someone told me that if you have bought the car with it already on it doesn't?? Then again, as long as you have the receipt from the last owner how would they know?
A friend of mine had a powerflow system on his Escort years ago, the welding was shocking. It really depends on the garage. The welds were also really rusty, so do some of them just use mild steel welds anyway??