I have been reading this with interest, and have a question. How do the manufacturers of these mills try to make allowance for a user's changing the height without losing accuracy? Is there a procedure to be followed incorporated into the owner's manual? A physical reference point somewhere on the mill itself? Some other feature or procedure of which people may be unaware?
They don't, assuming by accuracy you mean location. I've had one since around 1996. Using extended center drills, screw machine drills, and reamers with overlong (for my needs) shanks cut off combined with the 5 inch or so quill travel avoids the majority of height changes. You may still have to pick up a center or edge now and then but with some wiggling of the eyebrows and thought up front a lot of it can be avoided. Using an ER32 adapter for end mill and short tool holding is helpful as well. It's worth thinking about preserving some face / corner / edge to pick up in case a head shift is needed. Keep in mind you don't loose X/Y relationships as you would with shifting the workpiece on the table, you just loose the location of the spindle centerline and Z height information. Pick up ANY repeatable point on the work to get back in business, you don't have make it a big deal. Poke a 1/4 inch hole on an edge that will be removed down the line and pick it up with a 1/4 inch bit of drill rod. For most needs the accuracy will be sufficient. When it isn't, use better methods. A laser in the spindle will do a nice job to within a few thou with a small enough dot and a clean edge on the work. It isn't as though these machines have precision ground lead screws, almost every move of any length is adding or reducing error with respect to some other point on the work anyhow. Everyone thinks about accuracy above the table, few consider the inherent variations in the parts of the machine they can't control or even see beyond trying to remember to cross the backlash. No point chasing tenths when your handwheel graduations are +/- 0.005 " over the length of travel. You want sub one thou precision and accuracy, you lock the tables, set up fences, and grab the gage blocks. It's home brew jig borer time. Do that a few times and having to relocate the spindle center line feels like a luxury
Unlike a knee or dovetail column mill, instead of just planning on moving things when needed as the job proceeds, you think about how can I work without changing Z zero where Z zero is the face of the spindle with the quill fully retracted. The patron saint of round column mills is Wile E. Coyote or perhaps Heath Robinson / Rube Goldberg.
The two things that are a real issue for clearance are coaxial centering gadgets and boring heads. The best I can say is that on the rare occasion I need to use a boring head I'm already committed to raising the head, so I make room for the coaxial indicator as it's about the easiest way I know to find center of a large hole, namely the one I'm going to bore.
If affordable knee mills were available, or the now common "affordable" dovetail column mills existed when I was buying mine a round column would not have been purchased. You buy the best you can afford and learn to work with it, and maybe upgrade when you have to or can afford to.