After some digging I end up realizing that the issues thrown are still a reminiscent of this. Actually the btrfs check was founding issues related to the size of the physical partition contrasting with what btrfs thinks is the size of the partition. This was solved by momentarily shrinking the partition and only then moving it back, as it now does not believes to have a partition outside the limits of the disk.
My problem is solved but after trying this approach I’m still curious about the ways of having a cloned btrfs partition working.
Well while I don’t feel comfortable say that I’m an advanced user, the only reason why I pick those instead of something like Arch or even Gentoo is the amount of choices you have to make just to have a proper system working. I did experimented with those is the past, but nowdays I would rather stick with a solid starting ground and then build what I want from there. Also I find btrfs very interesting, and wanted to do something with it when I formatted this system 2yrs ago, so it explains how my choices led me here.
This is a point. When I was trying to solve this by cloning the partition I edited /etc/fstab to have the new UUID but despite that / was still booting from the old partition. Only the /home directory was accessible from the new partition which I found confusing and thus decided to do it by moving /dev/sda3 back.
I definitively will delve into that in the future to understand what happened but for now i have my disk working is I intended. Thanks everyone for the help!