Okay, I got a chance to look into this. The answer is oddly simple. Sublime Text does not by default know how to comment VHDL. The toggle comment command simply does not work at all, no matter what it's bound to. So I'm trying to figure out how Sublime Text knows how to comment anything! Maybe there's a file containing a language attribute that needs to be set that I never set (because I wrote my own command.) Anyway, I'm looking into this.
Final edit: I have a fix for this in development branch. You'll probably see a package update in a few hours after I make sure everything is clean and push a release.
In short, currently the header is generated with a sublime snippet. The lines you see in the header are not dynamically generated for your chosen line length. It could be possible to dynamically generate the header without using a snippet, however it would take some time to write that and I'm behind on my bug list as it is. I can add it as an open issue and consider it, but I don't see that getting implemented in the near future.
The line and box stutter typing shortcuts do pay attention to your chosen line length because those are dynamically generated.