I have analysed which cells overlap between Elsweyr Anequina and TWMP, and I found that they are exactly the same cells that also overlap between Anequina and the original Valenwood Improved - and all those cells are in Valenwood! Basically it is excessive padding attached to Anequina - this sort of thing can happen automatically in the CS. This is the reason why Valenwood Improved Original or Tamriel.esp for the TWMP version has to be loaded before Anequina, which seems counter-intuitive.
What happens here is this. These new lands have to create new cells outside of Cyrodiil because they do not exist in Oblivion.esm - they go beyond the existing padding. These new cells are created automatically by the CS when you scroll around the land, and the CS assigns them some formIDs. Naturally these IDs turn out different for the various mods, so if you try to load them together, you have multiple cell definitions for the same coordinates. When the game encounters this, it keeps the first definition that it finds and destroys all other cells defined for the same coordinates. So in this case the first definition overrides all subsequent ones, which is the opposite of what happens with everything else.
Destruction of a cell during load means that every non-persistent object in that cell is deleted, so the landscape, the path grid, trees, buildings, flora, rocks - all that is deleted, but persistent objects like NPCs, doors and markers are preserved. Disembodied doors, anyone? Yep, that's where they come from. It means then that it is only safe to allow unimportant empty cells to be deleted, otherwise you are erasing content and creating disembodied markers, people and doors.
Of course it is better not to force the game to clean up your mess. It is better to delete unwanted padding cells from the mod yourself, so that there are no conflicting cell definitions.
And this is exactly what I'm doing for my own game: trimming off padding from Anequina. The border between Anequina and Valenwood is quite clear, both in the original and in the TWMP version, and it is the same in both of them. Unfortunately Iliana is no longer replying to messages, so I won't be able to release this trimmed down version since it is explicitly prohibited to release alternatives to the main download, and cell deletion is not something that can be done with a patch. Besides, it is not strictly necessary... It's just something that I am uncomfortable with.