TBH the real issue would be pathfinding into / out of the rotating section.
Simplest way would be pipes or shafts - either the windmill’s gears pull/push/rotate the shafts, or they pump air/water through pipes, and you use that to power a machine nearer the mine. See Dwarf Fortress or Gnomoria for how you can use great big shaft/pump/etc mechanisms to transport mechanical power over long distances.
Agreed.
Well, having a hand crank option also makes sense. In terms of the mine being flooded though, DF has a swimming skill for its dwarves so they can avoid drowning, so it might not be the end of the world if you hearthlings bump into an underground water source.
Another thing DF does is tell you when it finds warm (and wet?) rock - indicating magma (or water) on the other side. That way you can quickly halt the mining and see about opening it up carefully, or digging around it etc.