Hi,
I had read your topic but didn’t know the answer. Luckily a similar question on merge strategies was asked today moving the knowledge along: How to ignore .gitlab-ci.yml file when merging the branches
TL;DR - the setting needs to done on the GitLab server itself, which is discussed in this feature request. I don’t know whether the mentioned workarounds really work. Maybe @Linds or @gitlab-greg can chime in here 
Cheers,
Michael