Short answer - yes. The PCM will alter the fuel trims in attempt to not damage the catalytic converters that are 'supposed' to be there. I drove around for months without MIL's; when I finally got them, it was a night and day difference.
I noticed not one bit of difference when my CEL was on and when it was shut off with my Diablosport tuner. Then again, I didnt even feel a gain from the Diablosport itself... so thats not saying much, hah.
I drove like that for a few thousand miles, wont hurt anything even if it does re-adjust the fuel trims to compensate.