For server projects, we suggest that you store a system model in the trunk and generate product versions in branches.
Lock elements
Make sure you can lock the model before transformation (you can see locks in the Lock View tab). Otherwise, the transformation will only be partial, and you will be notified about elements that could not be locked.
To keep the 150% model of the system, make sure you do not commit a realized variant to the trunk after the transformation. Commit a realized variant model to a branch or store it locally.