i have the giac chip w/ flashloader complete with stock program. when put on the stock program, the dealer sees the stock program if he checks.
this doesnt mean, however, that the software is invisible. 99% of mechanics wouldnt look any further once they saw stock software. the flashloader doesnt erase the upgraded software, meaning its still in the ECU.
with a little investigation the mechanic could discover your upgraded software.
on the other hand, i've had the giac software for several months and have been to the dealer several times with it set to "stock". they havent said anything to me.