It's pretty rare there are parts with "unclear" licensing. Does it happen? Sure. But "often"?
I'm fairly sure that almost all projects are receptive to updates for dependencies with security issues; I don't see why a distro needs to "untangle" anything for them.
> with system wide dependency you just update that and you are done
Unless the system-wide update won't work with your program.
The entire point of the Go tooling is that you can reliably and consistently build your software, and replacing random parts to create a weird unsupported (by the actual developers anyway) version is something the Go tooling was never designed to support: it goes exactly against what it was designed to do. Hence my previous comment: perhaps this isn't the best of ideas.