That's maybe not that easy. It sits on top of QtWayland which we have version 5.4, according to mailing list info. Don't know when xdg-shell was introduced and how to enable it.
As for keeping native look - I agree, that's better. Reasons for going for enabling flatpak support are several: get access to the latest Qt API (5.12, 5.13, and probably 5.14 soon); ability to use apps developed for other Linux platforms before porting to SFOS. Major advantage of getting latest Qt is access to the toolbox that can be used to write mobile-oriented web browser using latest engines. As many on official devices use Android browsers for it, I think having non-native looking but decent browser maybe better alternative.
PS: take my comments regrading Wayland extensions with a salt - I am not specialist in the area
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