Sage should use proper overlays

[collares]

Copied from #43755, which stalled: Sage has lots of dependencies and integrates tightly with them. Some of them have to be (temporarily) pinned at older versions. Currently that is done by simply using .override. But since there are so many dependencies, they are likely to depend on each other. That makes it necessary to "wire them up" using lots of inherit's (as seen in #43679).

See #43755 for a draft PR, #44196 and #51213 for possible solutions (which may have more modern equivalents already implemented in Nixpkgs) and #43828 for a rejected fix and accompanying discussion. The Python package set has a special variant of packageOverrides which could be an inspiration, even though the top-level packageOverrides is deprecated in favour of overlays.