There is no need to spend time on telling how super useful the MultiBranch Job is in Jenkins. However, there is one drawback; You can define and use only one Jenkinsfile in a given repository which will be the default Jenkinsfile for all scanned branches.
As this may sound complicated, from time to time you may need to use different use Jenkinsfiles in the given repository for different purposes. In this case, your only option is to define different Pipeline Jobs with different Jenkinsfile and branch settings.