I use a lead hammer around the shop for most everything. Light taps to adjust, heavy slugs to seriously move. It can be used or a scrap of 2X4 and a steel hammer if you don't like lead. Anything that won't bounce. . . For the MF-C mill, the process is the same as for the lathe and other vertical machine quills. I loosten a half rotation to one full turn and tap with the lead hammer. Then back it out by hand. Most times a 3/8-16, sometimes a 10mm. When the metric drawbolt is used it isn't left in the machine. I had acquired a piece of unplated all-thread, it rusts if I look funny at it even when oily. I use some odd setups making my models so some of my gizmos aren't "approved" for general machinist work. Tiny gears the size of my thumbnail don't need much clearance room.
Rereading the OP, the nut on the end of the spindle is just to hold the tooling tight. It's never an issue with the MT-2 on the spindle. I don't understand the jump from one end to the other. I loosten and tighten the nut with an open end wrench and never use the hammer there. There are occasions, very rare but there, when I remove the spindle with tooling intact. And I'm sure someone with two or more spindles might mount tooling on a second one in advance of a move. I only have one spindle, a 1 inch, but a number of MT-2 tool holders and gear cutter mounts. Things get swapped around some.
.