Update:
I suspected that the following locations never got marked as cleared because I did not clear them before major quest-lines involved them:
- Bloated Man's Grotto
- Bronze Water Cave
- Dustman's Cairn - this one was an error on my part: a couple of draugr never popped out of their sarcophagi, once they did and i killed them, the dungeon "cleared"
- Glenmoril Coven
- Knifepoint Ridge
- Wolfskull Cave
...and I have confirmed it (w/ exception of Dustman's Cairn, as noted above). Starting a new game, I went directly (w/o any quest connections) to these locations and killed the occupants and all 5 showed as cleared on my in-game map. I suspect that if they respawn after enough time has passed, you would also be able to clear them at that point - they simply cannot be cleared while they are in that quest-related window. The only exception to this might be Bronze Water Cave because it becomes physically connected to Irknthand (which is not clearable) after the TG quest. If you go in there beforehand, it is a closed off, self-contained cave with a couple of minor critters (a wolf and a skeever, IIRC).
Here are my findings:
The UESP says that there are 184 clearable locations here http://www.uesp.net/wiki/Skyrim:Dungeons#Clearing, but on their page listing clearable locations they say there are 189 clearable locations: http://www.uesp.net/wiki/Category:Skyrim-Places-Clearable... although one of them does not actually appear on your world map (http://www.uesp.net/wiki/User:Jak_Atackka/Sandbox2). I have definitely cleared all the locations on the UESP lists ('cept the Jak Atackka cell). The UESP states that Giant's Grove, while showing up as cleared on my world map, actually only counts as part of Fallowstone Cave. They also state that Clearing Skybound Watch Pass effectively clears both N and S Skybound Watch locations. They do not make any similar notes regarding Cold Rock Pass, Shriekwind Bastion, or Brittleshin Pass, although the same principle may apply. The UESP states that Angarvunde is not clearable, but it is clearly marked cleared on my map.
On my in-game world map, I have 196 locations marked as cleared (I can post the list if you like), but my character's journal states that I have only cleared 183. *My temples start pounding at this point*
I have 3 lists of clearable locations, none of which coincide with my journal number. I have UESP's list of 189, my world-map list of 196, and a custom list that tries to account for linked locations counting as 1 cleared location (e.g. Steepfall Burrow and Lower Steepfall Burrow = 1 cleared location) that adds up to 184.
I don't know what the point of all this is, but I will be doing 1 more playthrough, and - oh, yes - I will be keeping track...
P.S.: still waiting for info on how to use the "setlocationcleared" command - it didn't seem to work with the coc descriptor or the numeric reference from the CK.