First, this proxy is an excellent idea 👍
AFAICS, the JIRA DVCS connector in conjunction with this proxy will allow synchronizing only those repositories of the user that is used to connect from JIRA to GitLab ("Team or User Account").
Would it be possible to allow synchronizing repositories for an entire GitLab instance? It looks like one can list the repositories with GET /projects: https://docs.gitlab.com/ce/api/projects.html#list-projects
That way, one could synchronize repositories based on the permissions/visibility of the single user instead of configuring multiple DVCS accounts with different users.