Peco is available in SS if you don't want to deal with the paint issue. Or, before you install the Peco, strip the paint off and coat with something else. Honestly I have no idea what type of coating would hold up to exhaust pipe temperatures, which is why most mild steel exhaust systems end up all rusty.
If you're having a muffler shop install the system, consider what I did... Throw away the pre-bent pipes that Peco sends and have the shop make custom pipes from aluminuzed steel. It will never rust and has thicker walls than SS or mild steel. It is also less affected by heat change than either of those materials which means less chance of leaks down the road. Stainless is notorious for expanding and contracting which leads to leaks. I also recommend welding all seams. Clamps distort tubing and will always develop leaks over time.
As for the Falcon, I just pulled a Falcon SS off my GT and I'm much happier now. It's a fine exhaust system but the Peco is built much more sturdy (it weighs three times as much!) and I prefer the deeper, smoother sound. But that's just personal preference. Plus, I'm sure the Falcon Big Bore would sound different than the Falcon SS I had.
Rather than pay for the Peco SS system, I now have 2" aluminized steel pipe running from my header back (attached just behind the 2-1) to the steel Peco rear box, which has retained it's paint. Apparently the pipes get much hotter than the box itself which is why the paint peels.