I don't have an automated answer for the former, though it's probably possible to build something that dynamically generates the custom IDs in your account. Seems simpler to just have solid communication lanes between the dev team and the folks creating/updating Objects, but that definitely breaks down at scale.
For the latter, I checkout a new branch and run
suitecloud object:update
over all the Objects in the SDF project, then open a pull request for the branch in order to review the updates.