After another evening armed with a text editor and some mean Javascript, the commenting system seems to be behaving a bit better now. It now says whether you are logged in or not, and does so everywhere.
One last niggle remaining is the fact that the Name and other fields for anonymous commenting remain visible to logged in users, which might lead to confusion. Another dive into the evil bog that is Javascript will no doubt fix that.
For the cognoscenti: enabling the default Javascript from Movable Type solved most of the problems. The extra problem that created however, was that with the way I hide the comment form until needed, I hit some seriously weird Javascript scoping issues which took a while to track down and resolve. If any visitor loaded a page off of this blog earlier this evening and got a popup saying ‘Canary!’ - don’t worry, that was me trying to debug this thing :).
So, feel free to use the commenting system. If you run into a problem, you can always send me an email (link behind my name up there) or, just for the fun of it, why not comment it :) ?