Have you spoken with Arthmoor (he's working on the Skyrim Unofficial Patch as well as many other mods) about the problems with using an ESM as a workaround for the Navmesh bug?
I was reading earlier that Arthmoor has some strong arguments against creating ESM files (although I didn't take in the full details), and that they in turn can be causing other more serious issues for players later on down the line, so he recommends putting up with the navmesh bug for now.
Edit: Here's one of the threads discussing issues with Skyrim, and why some Quest mods don't work when combined - http://www.gamesas.com/topic/1374785-why-do-quest-mods-seem-to-not-work-with-other-quest-mods/
and the relevant part:
Onam Records are basically a list of overridden forms in an ESM. They tell the game which ones your ESM overrides in the parent files. Usually Skyrim.esm. They're a record type we have no reliable way to generate at present. The CK doesn't do this unless you work for Bethesda.
It's the big catch 22. Convert to ESM to fix navmeshes, break nearly everything else you've done in your mod. That's why the damn bug needs to get fixed. Folks with Twitter accounts may want to look into raising the issue there with the #navmeshbug tag. Keeping the issue in the forefront is the only way it's ever going to get fixed.
It seems that ESMs can not only break your own mod, but other people's mods too...