Maybe a contrived example but shouldn't Qt6 be answering with a compatible answer if a Qt5 app asks it what the theme is? And shouldn't the app be asking what the "theme" is, rather than what the Qt5-theme is? It seems like a fundamental issue with compat between apps built for different versions of Qt more than a problem with flatpak?

And is the sandboxing perhaps going a step too far if apps can't access the things they need from the environment?

If Linux libraries had that much respect for backward compatibility, there would never had been any demand for Flatpak. Flatpak (and snap) is merely a workaround for the lack of a common "Linux platform" with comprehensive, versioned APIs analogous to the Windows API or Android API. After all, Flatpak essentially provides a way to run a distribution (provided by Flatpak runtimes) inside the host distribution.