For now, between existing master branches of Qubes components and release4.1 ones, there is not (that much) differences but, in the next months, it will be the case, similar with release4.0 ones.
Since Qubes OS release 4.1 is officially here, I’m thinking to create a branch for the overlay in order to preserve compatibility with e.g. GUI protocol or qrexec. It is very similar to maintain two overlays where in master branch, it will simply follow every component master branches, whereas in the overlay release4.1 branch, it will follow qubes components release4.1 branches if they exist. For example some components don’t have any releaseX.Y branch because it’s not necessary like GitHub - QubesOS/qubes-app-linux-split-gpg: Qubes component: app-linux-split-gpg.
I’m opened to any suggestion and comment about this proposal. Notably, this is why I’m retaining since a month to not update the overlay.