There's always one guy who'll say, "Meh, close enough."  I suppose I'm him, here, but, at the same time, you're absolutely correct.  The Ayenbite that has been requested is another such instance.  (I think with Layamon the argument is sometimes that it the consonant became /y/ in his case, so modern editors feel like they're helping readers by making him more obviously Lawyerman.  All such things are excuses, though.)  Given that we are always already out of compliance with some browser or OS (e.g. does anyone know how far "Windows MediaCenter" or "Longhorn" are going to shove the old fonts out of whack), the kludge-y but best solution might well be to use an unusable typographical symbol (*, ^, #) and have a "Key" that indicates that that symbol was used for the yogh.  That would be the most honest way to do it, but it won't give the uninitiated any way to understand it.  They won't attempt to read it in their heads (assuming they can read thorn, eth, and ash now).  I just don't see how we can chase down the horizon with the reverse Procrustean effort of fitting everyone's bed at once.