The FQ360 maps are quite nice as they stand IMHO. The 360 just needs the boost curve sorting to make a bit more power (on the stock solenoids). I also think it is wise to add some safety back in to protect from overboost situations, as the 360 runs unachievable boost targets and limits
I believe most vendors just over write the 360 maps, which seems a shame as they are a good base tune to start from.
There is a recent similar thread in the ECU section:
http://www.lancerregister.com/showthread.php?s=&threadid=137195
If I were going the ECUTek route, personally I would certainly consider talking to Sam the Dentist.
I'm not sure the dealers - by default - can check the ROM image. I'm fairly certain the MUT tools do not have the ability to read the maps, but of course if they want to find out they will but they just don't normally have the software. Of course, they can get the software the same way as you or I can.
My dealer has yet to notice I've actually now changed some of the MUT requests
Apart from remapping the only other things I've done is de-cat, install a Walbro pump and modify the stock airbox slightly.