> Is there a sane way to record these sorts of variation in line indentation? (I'm not opposed to changing the way I'm encoding line indentation if that is the problem.)
I an not clear whether you are seeing a pattern in the indentation (every 5th line or something)? You could encode that with @type on the lg element maybe. If the indentation is apparently random, the @rend on the l element seems a rather normal way of recording it?
As ever, ask yourself why you are preserving the rendition. You don't/can't record everything about the appearance, after all.