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This is only tested in Firefox 91.4.1esr 64bit, against my Calibre-Web website but in this case it supports lookup for content in the embedded iframe and handles the iframe being removed and recreated when the browser window size changes. I have only tested character lookup because I have only used character lookup. In particular, I haven't tried any of the keyboard shortcuts to ensure they work for content in an iframe.
Much of this is new to me and I don't have knowledge or expertise to suggest that this is a good solution but it does seem to be working for me. If you find any faults in the implementation, I would be pleased to hear about them. Otherwise, I hope this helps you towards an enhancement to address the limitation reported in issue #85, should you be so inclined. And thank you for a great add-on, in any case.