Hunh. Same drill as the other holes, but these two holes are the last in the cycle? I'd have said thermal growth, but that's a ton of coolant, so unlikely. I too don't like the indents, and those could cause the drill to wander, but you said you've tried spotting those with a shorter drill bit, and no help? How about drilling through with a short (stub) drill bit, then sending the long drill for the bottom pair of holes? Do similar indent features exist on the upward face of the lower plate being drilled? How much material is the reamer taking off vs. the drill, and what kind of force do you expect for each...i.e. could you 3-step the process to get less force during the drilling and reaming, and maybe reduce the deflection of the part (assuming it's deflection causing the problem). Or try a slower advance?
edit: and thanks for the updates, pix and videos, that helps it become more clear. One more question, looking back at the photo posted yesterday, are there places where the drill sees metal (one on the visible top surface, and one on the lower part, but is there a hole going through the base of the pie-shaped standoff parts? Or are those pie-shaped pieces (kinda looks like a 4-jaw lathe chuck) solid all the way down to the plate of the 2nd part?