The solution proposed by the Medieval Nordic Text Archive
(MENOTA) is to put each word inside a <w> element, within
which one provides three separate renderings, each within
its own element: <facs> for the facsimile rendering, <dipl>
for the diplomatic rendering (in which the element <expan>
is used), and <norm> for the normalised rendering (this
obviously requires tinkering with the DTD, since currently
you can't put much of anything inside <w>).
To take a simple example, the Tironian nota for et, which
in Old Norse manuscripts usually has a form resembling a 7,
is represented by the entity &et;, which would be expanded
"oc" if this were in keeping with the orthography of the
scribe otherwise, but normalised "ok". The mark-up would
look like this.
I should add that I was not entirely happy with this model
initially (preferring something like <w reg="ok"><abbr
expan="oc">&et;</abbr></w>), but it bears an uncanny
resemblance to the proposals now being put forward.
For more information on Menota, see our handbook at
M. J. Driscoll