Bottom line on the tune is... Yes it will void your warranty if the issue is pressed. However, a good dealer/service department has allowed me to avoid the issue for 2 year so far. I do flash back to stock and replace the 2BAR MAP for any dealer visits (15 min tops).
Ultimately it is the price paid to play. Most dealers can tell if the OBDII has been accessed and when, but to find out what was done... (it could just have been a diagnostic read at home or AutoZone, etc)... requires more sophisticated software, which FMC has of course. Also, they should not be able to void the entire warranty...just powertrain. If you pressed the issue, the presence of a tune alone can only void the warranty, by rule of law, by showing that any failure was due to the tune... That said, FMC has a large group of lawyers on retainers and litigation is truly the spot of kings...see the bottom line above.
Personal feelings... IMHO: Tuning is the way to go and worth potential grief as long as you stay with one of the two experience tuners.... not that others can't do it... but several years tuning the same car I have without blowing up and engine and using shop owned SHOs speaks volumes to me. If you tune you'll never look back!