One thing that hasn't been mentioned is reamer/pilot spindle SIZE. A 6mm reamer with a group 1 bushing spindle on it is far more likely to deflect than a .308 reamer with a group 3 spindle. If you don't believe me, put a reamer between centers with a tenths DTI on a flute and push it around a little.

Indicator sensitivity is something else we should be talking about. If you're using the Interepid, you might be able to divide the .0005 divisions where the needle stops moving, but how much does it take to make the needle START moving? Will the Mitutoyo with a short stylus pick up imperfections that the long stylus miss? Is it possible that that letting the long stylus ride over the lands and come back to "zero" will pick up run-out in the grooves that would otherwise be missed if the bore was more circular?
Do a test. Chuck up a smooth shaft and clamp a short tenths indicator rigidly to the tool post at the end. Put the long stem beside it mounted off your favorite mag base with the flexible arm. Start pushing on the shaft and see which needle moves first. Do they come back to where they started? I bet your going to find that the long stem has more hysteresis than the short stem.

Indicator sensitivity is something else we should be talking about. If you're using the Interepid, you might be able to divide the .0005 divisions where the needle stops moving, but how much does it take to make the needle START moving? Will the Mitutoyo with a short stylus pick up imperfections that the long stylus miss? Is it possible that that letting the long stylus ride over the lands and come back to "zero" will pick up run-out in the grooves that would otherwise be missed if the bore was more circular?
Do a test. Chuck up a smooth shaft and clamp a short tenths indicator rigidly to the tool post at the end. Put the long stem beside it mounted off your favorite mag base with the flexible arm. Start pushing on the shaft and see which needle moves first. Do they come back to where they started? I bet your going to find that the long stem has more hysteresis than the short stem.