The new version of Mod Manager should hopefully be out today or tomorrow. ModMaker update will likely be the following day.
I am working on 3.2 of Mod Manager (next one is 3.1 Final) which will allow you to merge pcc edits through the use of patch files - this will also drastically cut down on mods like Ragdoll Armor and Hack All The Things as they are only like 2 byte changes.
With this, you can have a drivable atlas, with all enemies hackable, that can all be knocked down, all at once. The way it will work is that any mod that comes with a patch directory in it will migrate that patch to the patch library of Mod Manager, and then it will commit the patch to the mod, which will take likely a minute or two because it's extracting files with ME3Explorer.
Then you can browse the patch library and apply them to mods. Even if the mod doesn't modify that file, applying the patch will put that new file as part of the patch. After the first patch the clean file will remain extracted and it will not need to be re-extracted. Using this with the mod merging tool will mean that mods pretty much only can't be merged on coalesced differences.
This won't work with texture mods. I won't be supporting any files with texture mods, and it won't even attempt if the file sizes aren't right. Hex-edits don't change file sizes so this is fine.