When I tried Fossil it had things weirdly separated.

I was expecting when I make a commit, I would have the facility to specify what issues it addressed and it would close them for me automatically. It seemed there is so much opportunity there to "close the loop" when the issue tracker, etc and integrated in your VCS, but it wasn't taken.

This is a current architectural limitation, manifests (defining check-ins) and tickets are different types of artifacts and you cannot combine the card types into the same artifact. Changing this would likely break backwards compatibility with previous Fossil versions and I'd expect resistance. It may still be worth bringing up on the Fossil forum if you desire the feature.

Personally speaking though, I don't want things automagically closed GitHub-style based on parsing a check-in comment. An issue ought to be closed with intention.