The flagging of nonstandard MCAT scores is sort of a contentious area. The flagging of extended-time scores was recently dropped from the SAT after a big court case, but medical schools will see a * next to your MCAT score, indicating to them that you took the test under "nonstandard conditions" (i.e. not directly implying extra time). Supposedly, this makes adcoms pay less attention to your MCAT score, and look more at other factors (GPA, volunteering, etc.).
I believe medical school faculties (i.e. the AAMC) support the practice of flagging nonstandard scores, while the students (i.e. AMSA) do not.
The acceptance rates and later performance of nonstandard test takers has actually been researched a fair amount, try googling it. Last I checked, the overall acceptance rates for both standard and nonstandard MCAT takers were about the same, at just below 50%.
NB: If you take the MCAT once and do "reasonably well" (i.e. at least 5-7 per section), you will not be able to get extended time on a retake, even if your total score was very low and you have a medical professional document your need for accomodations. "Somebody has to be average," they'll tell you.
