Earlier quoted context omitted.
My personal opinion is that it breaks history and CI tests for all the feature branches. But at GitLab we encountered customers that insisted on having a linear history after migrating from SVN. Therefore there is a function in the UI of GitLab EE to rebase a merge request when accepting the merge request. See http://doc.gitlab.com/ee/workflow/rebase_before_merge.html
Could you expand on what do you mean by rebase breaking CI tests? I don't see how that's possible.
I've never found this to be an actual problem in practice.