Just so everyone reading know, DO NOT CLEAN FCOM COMPONENTS.
Generally good advice, mainly because the FCOM guys are aware of cleaning and have probably already done it.
According to Shikishima, no plugins that depend on ESMs should be cleaned either.
However, this is without merit. A mod dependent on a second ESM has no real issue to fear from being cleaned.
The ESM would have to be cleaned and all that mess, and that is really a job for the author.
An ESM with dirty edits is generally not kosher. There shouldn't be any real reason to edit vanilla records in one, without some very specific reasons - such as the way Frans edits into the vanilla leveled lists. Otherwise if it's a dirty edit, it's a dirty edit, period. I'm sure I'll be told I'm wrong about this, but I've examined in detail some of the claimed ones that should not be touched and I have seen no valid reason for it. Any hope of preserving something via an intentional dirty edit in an ESM is likely to be undone by half the ESPs on the planet, including the UOP.
For the most part, mod authors should be the ones to do the cleaning because they know the mod best.
True, and it's getting a lot better these days as awareness of the issue grows. Having come from Morrowind I already knew this was an issue to start with. It's even still an issue in FO3, and 99% of the time the modder has no idea the CS is making junk edits.
There are also certain highly outspoken individuals who will claim cleaning absolutely breaks everything about their mods. No verifiable evidence has ever been provided to prove this. One would be very hard pressed to provide anything solid to suggest gross dirty edits all over half the landscape and path grids will have any impact at all, other than deliberately causing compatibility issues with everyone else's mods.
Re: BAIN - It makes sense to package the cleaned ESP with the original archive. BAIN won't sit there with it's orange square telling you something is in conflict that way.