Just an update, I've had a little free time today to look into this a bit more and a program called tiki seems to hold a load of features for what I'm looking at, another is b2evolution. Just to point these programs out to see if anyone has had any dealings or to help others on the track I'm currently on to find what they're looking for.
Not sure if this applies to your situation but if your "low traffic sites" are similar to ours: we had hundreds of wordpress installs + hundreds of static sites which I all migrated into a single b2evolution install. This CMS handles the domain name -> website mapping pretty efficiently.
I have 300+ domains per server, each with only 1 simple LAMP stack + 1 CMS installation to maintain.
For the migration work, I outsourced the repetitive tasks on upwork.