I am very new to MMV and having so much fun after wrestling with Touch Designer for a while.
One thing that is a little annoying is having the ISF modules within their own folder i.e. I have to go into the ISF folder before I go into an effect folder before I find the effect.
Welcome to the forum. There's no problem if it works for you except that if you ever reinstall you'd have to do it again and you'd be a bit out of step with most other users. Also there's a muscle-memory that you'll get used to in this configuration and your mixing core (mostly binary) modules with less-core nodes, though I'd agree that many of them seem core. Maybe you'll start a trend.