Is there any way to specify that a room should contain a named monster? (As in the kind generated by Evil Chests and some Inconsequentia quests, not one of the predefined minibosses like the crab king)
Nope. Closest you can get is the <horde> command, which designates a group of monsters as a platoon and makes one of them the leader.
You should be able to. Look on some of the core files on the lower floors, with the corrupted Krong altars.