Well - was a little late upgrading from 39. Long story short: As recommended in fedora magazine, I finally first upgraded from 39 to 40 using the command line rebase
like in How to rebase to Fedora Linux 41 on Silverblue.
And then again from 40 to 41. The process went both pretty fast and smooth, despite having a bunch of layered packages like:
… rpmfusion-free-release and rpmfusion-nonfree-release as well as akmod-nvidia.
I first did a rpm-ostree reset and after reboot then directly upgrade from 39 to 41 and ran into issues with akmod post processing scripts.