Don't they protonate / deprotonate in order to change color, thus raising or lowering the pH of the solution (even just by a little)?
Yes. pH indicators are usually weak acids, so the introduction of a pH indicator would cause the solution’s pH to very, very, very slightly decrease. This minuscule decrease would have no practical effect on the reaction.
On a slightly tangential note, pH indicators are somewhat imprecise in that they depend on people’s subjective interpretations (“has the color fully changed?”). That’s why many scientists prefer to use a pH meter.
None of the information above will be helpful to you on the MCAT, though. On the MCAT, the pH indicator is just a tool for measuring a solution’s pH, with no meaningful effect on the solution’s pH or on the reaction. I hope that makes sense. Best of luck with your studies!