There a few inherent problems with this type of system, so it wouldn't work for all circumstances.
Here's the problem with using the MAST records to cross-reference assets... If there's a loose file that is referenced by both a vanilla game plugin asset (easily filtered out), and the modder's plugin, and the asset doesn't belong to another modder (a custom override), we'd want to include it, otherwise no. Therein lay the problem; how to tell to whom the loose file belongs. And vice versa.
If a modder's just testing his mod only, the system would, at least to the point of including custom assets that aren't found in any of the plugins. Then there's no way it'd know to include those. Unless, we auto-add all custom assets- but the modder would have to be careful (like adding from the games "data" folder instead of a separate mod folder). A way around this is to keep the modder's custom assets in a separate folder and sym or hard link the game to the files. This would allow auto-adding the entire folder, and checking for missing assets, and bypass the need to sync to dependent or master plugins; what's in it's separate folder is what it uses, otherwise report it as missing.
Plugins can be specified in one of two ways; specifically using the "-p" parameter (no limit), or within a folder using the "-f" parameter. If a folder was specified, the utility loads the plugins from the 'root' of the folder specified (presumed to be "data"). Either can be used simultaneously or interchangeably.
Without doing much modding, I'm guessing the normal procedure would be to place the modder's custom assets. plugins and BSA (if present) in the games installation "data" folder (so to speak) for testing. From there, just select the plugins, and the utility will do the rest, but, if there are assets whose names aren't found in the specified plugins, there's no way the utility can pick those out- thus back to a sym or hard link solution.
What's the normal procedure modders use when creating and packaging mods? This might help me to find tune the process better.