Thanks to Harry, Michael and Peter for their responses. It all sounds
embarrassingly straightforward. On reflection, entities are the answer
for minims, too, e.g. &minim.
Michael suggests that the use of multiple symbols doesn't appear to be
ambiguity. The problem arises when the transcriber is unable to identify
a character which may take several forms, some of which are similar to
the forms other characters may take. The current process is to scan by
eye the page looking for other forms which look the same. This procedure
falls down when no known word seems to contain the ambiguous form in the
appropriate location, and is time-consuming. The example provided for
encoding readings seems to assume the need to choose between a limited
number of seen possibilities, rather than possibilities that are
unperceived because of difficulties reading the letter.
It would make sense automate the search for letters described above,
possibly tied to a dictionary. Entities could be used to represent
different sets of topographical features. A similar procedure would be
followed to disambiguate minims, e.g. to help decide whether
&minim&minim&minim represented 'ui', 'ni', 'm', etc., by pulling out all
possibilities from a dictionary.