Stuart > If you upload an HTML page it's essentially the same as uploading a Word document or a .pdf (an external resource) - and the Glossary cannot automatically link to words within those.
Wrong information! It is quite possible to have autolinks in uploaded HTML documents in Moodle. I do it all the time. To obtain this facility, you must select the correct setting in Administration ► Modules ► Filters ► Manage filters.
Joseph