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.