Such is very much like contextual menus, e.g. right click. Having to go to some main menu, either from some other app, or here the viewer menu, I think is extra noise and delays user choice. Contextual menus were invented for a reason.
As for the double click or long tap, it seems that if one selects text, or single clicks on a highlight, it is likely one wants to act on it in some way, thus all apps I know of behave as suggested.
btw, unsure what happens if one renames the file. In calibre itself, changing metadata, I assume records change. Outside of calibre, maybe some checksum is stored such that on EPUB load, it verifies if it's been renamed and could migrate highlights to linked file? If not, maybe a good idea.
another note, concerning a previous request to more quickly prepare epubs for viewing. If a file has changed but location is the name, any harm in unzipping with only changed files? It'd be quicker. I'm not sure what happens with new files, and deleted may need to be verified. But the cache is refreshed eventually so maybe little harm. Unzipping takes a long time, and I'm constantly editing with viewer window and PDF side by side, or using the viewer to proof and then correct.