You can copy the .nwm files from the original campain to your Modules folder and rename them to .mod. The module updater can find them there, and you can play them from NWN by selecting 'other modules'.
This might be a solution. Is it still possible to transition from one chapter to the next, or will this require exporting characters just prior to when they would transition to the next module, exiting and loading?
When you load the modules as 'other modules' they will transition you into the official campain ones at mod end, yeah. If you do it like this you'll have to either save characters or modify the modules's dialogue to direct to the correct follow-up module.
Personally, I think keeping two /nwm folders and renaming the one you aren't using is the easier option for this reason. (mind the difference between the nwn and nwm folders: nwn is the full install, while nwm is the place it keeps the original campain's module files. This is the only thing you'll need a copy of to have a second set of OC module files.)
At runtime, must the file names and extensions be as they were when the Module Updater was used on them? If not, then could I take the above steps, but then use those files to replace the .nwm files in my second NWN directory?
The module updater is something you run once to change the files. It doesn't care what you do with them afterward.
Module files saved as .mod will be recognised by the game when they are in the /modules folder no matter what their names are. The module updated will find them here.
Module files saved as .nwm will be recognised by the game when they are in the /nwm folder with their original names only. The module updater will find them here.
So yes, you could take the files from your second nwn directory, rename them as .mod, place them in /modules, update them to use the prc, change them back to .nwm and place them back into the /nwm folder of any nwn installation.