You should be able to comment on any block-level element. So if each line is a block level element, then you'd be set. They probably aren't block level elements, though. The comments use a Very Little Language to identify what element they were attached to, anchored on something that can be found globally and hopefully is stable (typically an element with an id). Right now when you double click it walks up the DOM tree to the first block-level element it can find; potentially that could be configurable so you could comment on smaller elements.
Another option would be for the path language to know about named anchors too (I've meant to add this anyway), and for it to also stop on named anchors even if it is looking for a block-level element. And then, if you put a named anchor in every line of your code (nice anyway) it can be commented on that way.
I've actually also thought about Trac as well, as this seems relevent to a lot of what Trac does. So I definitely hope they can work together in some fashion.