Another couple of options:
Machine the tops off the cap heads a little. The hex recess will be shallower, but you are not tightening them to three grunts.
Investigate low head cap screws. They are a legitimate product, but more costly than standard capscrews.
If you look at YouTube videos of Cutting Edge Engineering Australia, he has a line boring machine. The heads of the cap heads holding it together face the thing being bored. They are in through holes, so he has made a screwdriver slot at the 'tail' end so the hex key is only needed for the last 1/4 turn, a (potentially power) screwdriver being used for the rest of the movement. It would mean converting the female threaded holes in the chuck to through holes, but they could be of a small diameter to suit the screwdriver.
Gluing the spacers in the counterbores means you need one spacer per counterbore per chuck. Gluing the spacer onto the securing nut means you need only one per fastener. If used on a nut and stud, it has the same benefit as the unthreaded section of stud suggested above.