The age old question-- the easiest answer is: It depends. Your experience will be based on the dealer and your relationship with them. Here are some facts:
1) Dealers are trained to look for tuner stickers. So if you do get a Cobb AP or anything of the sort, you shouldn't go around putting the sticker on the back window.
2) Bolt on mods are easy to spot (your CAI/Borla Exhaust). Depending on your relationship with the dealer will depend on how they react. You can look at a bunch of stories on here of both horror and success. It's much easier to spot a CAI vice a tune.
3) ...but a tune is not "hidden" even if you flash back to stock there are ways and traces to see if you've tuned the engine via the ECU. Will the average service look for a tune? Maybe?
4) MM works but it isn't a get out of jail free card. A dealer doesn't have to PROVE your modification caused the fault, just that the fault COULD be attributed to it.
This all said, I'm tuned, and for the Ford Exec's reading this my vin number is...hey,
@911 Crazy can you post your vin real quick.....
I don't regret it. It's pretty easy to undo and if you go with a reputable tuner, who has millions of dollars of R&D, you probably won't have issues....
TL;DR: It depends on a lot, buyer be warned.