Concerns with Mining (Both the department and Z-level)

[ISaidNo]

That's my biggest concern here. The move of the magnet to the station, and presumably its reassignment as the primary mining method, would make it a target, collateral or otherwise. One bomb hits that bastard and no more mining.

Not true. The mining fabricator can make magnet replacement parts which, while expensive, can be used on an empty magnet chassis to make a new magnet. The chassis should also be indestructible from anything short of a black hole. If a black hole DOES hit it you've probably got way more serious problems than the lack of a magnet.