No I hardly see even for a user that this is easier than just
1. downloading the original packages for your package (and choosing only what you want).
2. Unzipping them to one folder that is numbered and named.
3. taking out and cleaning any offending esp files then putting them back (possibly redate the esp too).
3b. if necessary rearrange complex archives to be BAIN friendly.
4. Zipping up that archive and copying or moving the archive to BAIN folder.
5. Installing or annealing.
While the BCF might handle simple replacers well it would fall flat with mods with optional (yet named the same) esp files, body mods, or even basic archives that still needed cleaning.
Then what about updating the archive sub-packages? Would you put all those packages back in the data folder to repackage only one update?
With my method you would download the update and only unzip that to the destination sub-package then rezip. Admittedly that could be a pain, but not as much a pain as re-adding all the packages to run BCF again then take those out. See the ting is if you're just going to have to ever re-add the packages to the BAIN folder then why ever take them out?
I know I'm no lazy ... but the reason I'm no lazy is I don't want more work later.
I vaguely recall Wrye adding this as a request.