As noted in the thread you linked, Evan appears interested in seeing a reproducible example of the problem. I imagine he’d accept a fix for this in a future version of elm/browser if there were clear examples of how the current implementation breaks (if you have some, you should open an issue against elm/browser).
As far as workarounds, if it seems like Elm controlling <body> is the problem, you could switch from Browser.application to Browser.element. (I think this was also all covered in the other thread you linked.) If you still need control of the page title and/or need to interact with navigation commands, you could do that with the help of javascript using ports. (Though depending on how much of the SPA stuff in Browser.application you were relying on, that might get to be quite a bit of extra work.)