The "loading things thing" is the most important function of BAIN. Total awareness of all files in the DATA directory, where they came from and the priority level (in terms of overrides) of each.
Eliminate it and you might as well not bother with BAIN.
As for BAIN in FCOM, the basic fact of the matter is that the people in charge of the FCOM mods right now are too busy working on the mod itself to invest time in restructuring the archives, re-writing the install directions and dealing with the learning curve for a new type of install. That has to be accepted, not complained about.
That said, I am planning on making BCF files for the next releases of the FCOM mods that are under some control of the FCOM team. I will also attempt to write some basic install instructions for the resulting BAIN'd packages. I'm nearly certain I can convince Corepc to include links to the BCF files and the instructions in the FCOM threads and on the FCOM download pages.
When people start using them (hopefully) we'll see where the problems occur, and I'll try to improve them. With enough improvement, they may be able to go "official". Someday it may even result in the BAIN archives being the primary ones, if time is found to rewrite all the documentation.
However, due to BAIN having the BCF function, it's more likely that it will remain an optional extra. It's easier that way.
It's also important to note that BAIN is best at installing Resources. It's no better at installing ESPs and ESMs than doing it manually, due to an almost total lack of scripting. It will happily install completely conflicting ESPs and ESMs as long as they are "valid" by its standards. For installing ESPs and ESMs, OBMM is still king and OMOD conversion scripts are available.
If BAIN gets scripted installs, and someone writes comparable scripts for it, then it will be the best option by far, but it's not there yet.