I would grind the top of the tool, you would not be losing much so far as the longevity of the tool is concerned, they last for many years in regular use, so far as know, all the cutter numbers have the same vertical dimension, even the ones for acme threads, and they are the same for all tool holder sizes. Both of the setscrews are used to adjust for helix angle, I just do it by eye, nothing technical is necessary, both should be snugged up to eliminate slop in the allen bolt that secures the tool to the holder. I would guess that the holder would be too hard to machine the bottom, At least for most hobbyiests.