However, that doesn't seem to be any better in any other web CMS, and Moodle is extendable with lots of open source plugins for any imaginable purpose, so overall it's a powerful Swiss army knife, and it has all the advantages of a self-hosted, open source project.
I suspect the 80/20 rule is in play, wherein each of the 80% of users is using a different 20% of features so your choices are to end up with something nearly feature free (think early github issues for a ticketing example), something specialised to a specific vertical subset of the potential use cases, a complex and usually clunky GUI, or programmatic style configuration that requires a level of time investment that rules out the people whose jobs will be to actually use it being the ones to set it up.
Moodle goes the lots-of-features GUI route and does a less annoying job of it than average - like I say, I think the problems are kinda inherent if your goal is to support as many different purposes as it does, and that's a trade-off that's often worth making.
Thats what SQL is for. You can setup everything using their fairly simple tables, and keep it in sync with whatever registration system you're using.
Permissions however were confusing and forget about faculty understanding them.