Deploying with Capistrano (SCM Best Practice)

This is a general question on Capistrano.

I keep my bedrock repo and the roots theme repo separate. In the case the theme moves to a regular wp install the file changes and history are still there.

Would this affect my ability to deploy project via Capistrano?

It would since Capistrano technically only deploys a single repo. To me the solution here is to make your theme into a Composer package and just use it as a dependency. Then when Composer runs during deploy it will install it.