I believe Torrello was pointing out the fact that OBMM does not have the capability to maintain different files, from different mods, at the same time. (The same can be said true about vanilla files because even if you decide not to overwrite a vanilla file from an OMOD install, it can be deleted later when you choose to uninstall it.)
OBMM has some capability, but this is certainly a strong-point of BAIN. My point is that this BAIN advantage is not enough by far to support blanket statements of needing to switch from OBMM to BAIN,
For the sake of the argument, say you install OMOD X that adds or replaces some texture file. Another mod, Y, also has a different file in the same location. If you install one over the other, the last one installed is the one you get.
...though you can easily decide to keep mod X textures instead. OBMM warns you that Y will overwrite textures from X and asks you if you will overwrite or keep. Not by far as good as BAIN in this regard, but still more than adequate for most users.
Only that you cannot keep track of the order in which they have been put into place with OBMM. It gets worse if there are more than two mods that touch the same file (- and there are, just play with better cities, blood & mud, QTP3, QTP3 for blood & mud, and AWLS for the cherry on top). Once you uninstall any one of the OMODS that contain that file, it is gone. If you still play with the mod X or Y that uses the file A, you get purple mesh in game.
Now this is just plain wrong. You obviously haven't tried it.
What happens is that OBMM keeps track of the fact that the resource is owned by all the omods, and will not remove the resource until you have uninstalled all those omods. The difference from BAIN is that BAIN also keeps track of whether you uninstalled the one that you overwrote the other resources with, and if so revert to the older version, while OBMM only knows that the resource is shared and therefore keeps the last installed version.
I believe this is where BAIN can be called superior to OBMM mod installs.
Better, yes - but OBMM is evidently much better than you thought, and more than adequate for most users.
Again, to make myself clear, BAIN's handling of conflicting resources is definitely better than OBMM's, but OBMM's handling is good enough for most conflicts, and for most mod users it is very seldom to repeat install/uninstall of mods with conflicting resources. I'm not trying to talk bad about BAIN, but just don't accept that OBMM is not a very good tool for resource installation too.