I am a bit astonished we discussed it here about a dozen of times now (sticky????). Yest the problem are the portal & roommarkers which are affecting strangely GECK.
Simply move them out of the way ( z+5000 for example) press F5 to refresh the render window, make your changes and then put them back in place.
The last step is to clean the changed room & portalmarkers with NVEdit.
That's pretty awkward, I wonder if Obsidian had to deal with this too? But I guess they added the portals last and then didn't have to do anything with the level anymore...
It seems pretty pointless to me. It's not like any level in New Vegas would be too heavy for the GECK to display at once, especially since it doesn't have to calculate NPC AI and sounds and all that.