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Have you tried putting a link with an ampersand into the application and then trying to click through on the link? What I am seeing is that the & is being escaped by the application. If you copy and paste custom code into the application go back to the WYSIWYG editor or save the page as an HTML file the link is broken.
Looks like you’re not using the latest version of Publii. I’ve just tested Publii Version: 0.42.1 (build 16233) on Apple Mac OS, using the WYSIWYG editor. Everything works perfectly. Question marks in URLs are maintained in place.