While the party cannot leave the dungeon and come back, they could certainly try to rest in the dungeon via rope trick or otherwise. However, I would fully expect the rat demons of the dungeon to make regular rounds to ensure everything is okay. Finding a rope dangling where no rope should be would be quite the giveaway that something is amiss. This is likely to go very badly for the party.
So, it is in the PCs' hands, but I would strongly encourage them against trying to rest in Bonekeep.
As far as the rest, there are no restrictions on extra-dimensional spaces, mists have a miss chance for the enemies, knowledge DCs should not be increased beyond typical (rare creatures), etc. Bonekeep is plenty challenging as it is written - there is no cause or basis to invent additional rules.
Like all scenarios, run as written.