This is not a problem.
Create the repositories for the 'non-existant' systems and change their 'provisioning' and 'deprovisioning' tasks to custom ones which direct notifications / workflows to those who are actually doing the work.
When they are eventually connected, all you'll need to do is change the provisioning / deprovisioning tasks on the repository and the work gets done automatically. The users see the same process for all apps and won't know if they're manual or automatic.
Note - this is very high level - there will be additional work (setting up privs for the systems etc)
Peter