Any workaround (webextension is not an option) ?
every time you allow opening the link, you allow the site itself to load URLs for that protocol
Don't really understand what he's saying here?
So anytime I click my bookmarklet... what?
The site I am on when I've clicked it... what?
Can load URLs for that protocol... - which means just what?
That "protocol" (es:) only exists within the realm of Everything.
And there is no "URL loading".
There is only the passage of a string of text from one application (a web browser in this case) to the Everything (search engine).
(And all that does is to search your computer for a file name, partial or otherwise, of the passed text string.)
(A simple, though hardly efficient alternative [to automating this via a bookmarklet], is to manually copy a string of text, say from a web browser, & paste that string into Everything.)