If this description is accurate, the obvious workaround would be to create a .esm to hold any nav meshes. In my opinion, .esm files should be used for new content (where load order does not matter), and .esp files should be used for override content (where load order matters). So either the final sentence here is misleading or the problem description is misleading.
Neither. The problem specifically describes navmeshes in ESP files. Using ESM files cuts off an entire avenue of mod distribution that Bethesda themselves went to great expense to initiate, and went to a great deal of trouble to have us test in a private beta round. They've also themselves specifically said it's a bug that needs to be fixed and have stated publicly that they're working on.
Use of master files to dodge bugs is by definition a bad practice, so no, that's not an acceptable solution. If it was, it would have taken Bethesda very little time to simply allow the CK to save ESM files and solve a whole host of other problems in the process along with it. Clearly since they did not pursue this, they don't consider your idea of "best practice" to be the best practice.
"http://www.gamesas.com/topic/1347249-unofficial-creation-kit-bug-list-2/page__view__findpost__p__20325586 "
If this one is really fixed, why is it still on the list? The last update to that list was 01 March 2012. If this is the list of bugs that Bethesda is supposed to be addressing, basically, you are telling me that Bethesda is being more responsive than the modding community.
Because the person who owns the thread either hasn't been around or hasn't been willing to cross it off yet for some reason. Yes, Bethesda is being more responsive than one member of the community who isn't active at the moment for reasons he did not mention to anyone. It happens

"http://www.gamesas.com/topic/1344939-things-disappearing-in-the-world/page__st__30"
This one does not make sense to me. Objects disappear in the distance so that the game can achieve good performance. So this is not a description of a bug, but a description of a design trade off.
No. You've misunderstood the bug. This one manifests when you place a building and then try to walk up to it in the game. It will vanish if it's size column in the CK is > 1024. You will typically run right through where it should be, but sometimes the collision remains behind. For whatever reason, checking the "Is Full LOD" box fixes the issue as a temporary workaround.
"http://www.gamesas.com/topic/1345519-creating-new-worldspaceshow-to-get-around-the-broken-ck-features/
I'm not a worldspace modder and haven't messed with this, so I'll let someone else field the whys about why this is a bug.
"http://www.gamesas.com/topic/1347249-unofficial-creation-kit-bug-list-2/page__view__findpost__p__20321917"
First, because this isn't a height issue. It's an east-west issue. Note that it doesn't manifest in a north-south line.
Second, it's definitely a bug. Easily reproduced, and wasn't present in prior iterations of this engine. Bethesda has flat out said they won't fix it because it's buried in the Havok code.
Also this isn't a new engine. That should be patently obvious to anyone who spends 5 minutes either playing or modding the game. It's Gamebryo, in all its ugly glory.
The problems and inaccuracies that I see here are seem more likely to hurt modders than they are to hurt Bethesda.
Nobody ever said it would hurt them more than us. The fact remains though that many of the bugs on that list are legit issues, though some no longer are, and yes, we as a community have a tendency to jump from initial report to verified disaster a bit too quickly. It makes us look like idiots sometimes as a result. So I do agree we need to do better. One way in which that can start is to clean up that bug list by going through and determining which ones are really still broken. It will probably require someone who is around more to take over the thread too.