I agree there appears to be two bugs here - the old runtime bug which could be gotten around by esmifying the plugin, and a new one caused by the CK producing a flawed plugin. If you edit a vanilla navmesh and the mod index of the override is changed to that of the plugin - that's a serious structural error. What you end up with probably in-game is two un-connected navmeshes sandwiched on top of each other, each with their own conflicting NAVI records there to confuse the engine and break pathing. This definitely needs to be fixed.
And if those two navmeshes have the same data, they likely are cancelling each other out.
It seems to me that there are some fundamental changes to how data is handled between ESM and ESP this go around. Maybe the changes are intended to allow for a lot more to be done with the CK, but the way they were done presents a lot of new ways to mess something up if the modder isn't double-careful. An example of that is how scripts are no longer ESP-specific. If you mod a vanilla script and it gets compiled, it is altered for good if you didn't back up the original, and those changes persist whether the mod they were intended for is active or not.
I don't know...
I do know that there are a lot of awesome mods that can be accomplished even with the navmesh bug. Continueing to rant about the issue will not help get it fixed any faster. For now we should simply accept that this part of design is broken and proceed with other parts. For my part I have put up statements about the bug on the video tutorial list I maintain here and on the Wiki, in the written tutorial itself on the Wiki, and in the comments on the video tutorial BGS put on Youtube. Several have sent messages to Gstaff about it. And I will go ahead ant reveal that I notified Joel about it as well. THEY KNOW. WE KNOW and ANYONE WHO READS THE NAVMESH TUTORIAL, VISITS MY VIDEO TUTORIAL LIST, OR VISITS THE LIST ON THE WIKI WILL KNOW.
The direction this thread is beginning to go is one that leads to a "Let's rip BGS a new one!" situation. That will help NOBODY.
They posted yesterday that they are paying attention to the community and they are working on fixing what they can, and that they will continue to make updates for both the developers and the modders.
That's the official statement from them. I suggest that we take them at their word on it, let them work the problems and find the solutions. And in the meantime, let us make what mods we can make. Any release notes we release with them should include the list of known bugs with the game and a statement that we do everything we can to work around them. There's nothing WE can do about this issue. I cannot speak for anyone but myself, but when I face an issue I can do nothing about, I simply adapt to it and ride it out, hoping for the best. Worst case scenario being that BGS cannot fix this issue, community modding for anything other than stat changes dies out. Neither BGS nor this community wants that to happen. So God willing, it WON'T happen.