It feels like there might be two different uses of "coupling" here.
The linked article argues that GitHub locks in users by not storing everything in git, which what the post you're replying to is skeptical of. (I am, too.)
Being able to say "issue X has been solved in commit Y" is coupling the issue tracker and source control at a user experience level. The back end solutions are immaterial; they just need to be talking to one another, whether it's through plugins, or through proprietary features like GitHub already has (in which commits can be automatically linked to issues and vice-versa, merging PRs can automatically close issues, etc.).
The linked article argues that GitHub locks in users by not storing everything in git, which what the post you're replying to is skeptical of. (I am, too.)
Being able to say "issue X has been solved in commit Y" is coupling the issue tracker and source control at a user experience level. The back end solutions are immaterial; they just need to be talking to one another, whether it's through plugins, or through proprietary features like GitHub already has (in which commits can be automatically linked to issues and vice-versa, merging PRs can automatically close issues, etc.).