Certainly there is a lot of room for improving links and padding. Have you considered contributing them to GitLab? To get started see https://gitlab.com/gitlab-org/gitlab-development-kit

Having people pick custom fonts might make it hard to get the design right for everyone.

Reapplying changes in Omnibus is hard since it is shipped without a git repo, so you can't use git stash or git merge. You would need to switch to an installation from source but we don't recommend that.

I really hope you can contribute the changes you would like to see, GitLab's frontend can still use a lot of polish.