In the EE there is a new CopyArea function that would let you create a copy of an area that is in the module. It might work if the area files are in the override folder, but I haven't tried it and the Lexicon page for the function is a stub. For a player, the less stuff that's in the override folder the better, so you're better off integrating that content into the module.

Unfortunately, it's not enough to add a new area to the override folder. The area list in module.ifo also needs to be updated, otherwise the game will detect corruption and abort.

One way of creating instanced areas in EE is to use CopyArea to create the instances in the toolset (thereby achieving integrity in module.ifo) then use moneo, gffeditor or whatever to edit the instance contents to your heart's content (i.e. without having to use the toolset for editing, which presumably is the point).

The main reason I wanted to do this was to avoid module instability. I remember in the past, once my module was 70+ MB, with 300+ areas, the server would start using a ridiculous amount of CPU load in all cases (idle, combat, path finding etc). Removing all the areas and creating/deleting them as needed was the main method of preventing this issue from ever happening.

Did Beamdog at the very least fix this type of instability?

That problem is likely caused by memory issues; NWN is a 32-bit app so the 4GB ram limit is in effect. Also, areas with no PCs in them still contribute to system load since area heartbeat scripts, scripts associated with any creatures in the areas, etc. are still running even when there are no PCs in those areas. Beamdog is working on a 64-bit release, if/when that becomes a reality it should solve the memory issues.