You simply can't, both Lemmy's and the TR64 OGL plugins are exporting only what's loaded in their video memory, most N64 games are made like that to avoid getting too much things in memory to be sure also not to get any lag or bad FPS. Games such as Goldeneye, Mario Kart, Perfect dark are working like that.
Games like Mario64 , Zelda oot (not always) can sometime dump the whole thing (because everything is loaded already and is not using much polys/memory) , like bob-omb battlefield, the Hyrule field , etc.
If you want complete levels, just make multiple dumps are different locations of the map , merge them and remove duplicated stuff. Also, sometime, being at a part of the level where you can almost see it fully can also help a lot.