Delayed response sorry.
But basically the ford racing warranty is a seperate warranty that takes place of all parts affected by the frpp tune (so your engine basically). It's a 3 year/36000 mile warranty. After that, you will no longer have warranty coverage on anything said tune affects, though you'll still maintain warranty on unrelated parts. It would be same thing with your extended warranty, non-affected parts would maintain warranty while affected would lose it after the frpp warranty runs out.
I've heard on and offs about Ford being pretty strict. A guy on the facebook group said he had his warranty voided from an intercooler, which is sad giving how shit the stock one is. Nick's dealer seems to be more friendly though and that's where I plan on going in the event of anything major.
In a nut shell, most people just go the Cobb AP route and just flash back to stock for dealer visits, this way you maintain your original warranty. Cobb (and the tuners) claim their is no way for Ford to be able to tell your car is tuned, all the flash does is trigger a code for battery disconnect that will go away after a couple key cycles.
Here's a thread from the ST forums with some info on the FRPP warranty stuff.
http://www.focusst.org/forum/focus-st-maintenance/18533-official-ford-racing-warranty-thread.html