Restoring system databases on Availability group replicas I'll start this off by saying I'm very new to availability groups.

Looking at information on availability groups, it looks like you can't add system databases to a group. MSDN seems to indicate that we should manually replicate logins, jobs, etc. 

Are there any consequences of restoring system databases from backups taken on a primary replica to a secondary replica in an availability group?
All of your server configuration is stored in the master database along with your users logins so I wouldn't recommend restoring the master database from the primary.

As for copying users and jobs, have a look at dbatools . Its a set of Powershell tools that include ones for copying users and jobs.