Separate Transformations for SepTop

Thank you for all your work and dedication to this project,
Is your feature request related to a problem? Please describe.
I really like the fact that the HybridTopologyProtocol allows you to save the complex leg of the cycle and the solvent one separately. This makes it easier to schedule the partitions for submission to HPC environments, and to experiment new approaches in one environment only.

Describe the solution you'd like
Is it possible to do the same with the SepTop protocol? I read in the user guide that "both legs of the thermodynamic cycle are constructed and run sequentially in the same ProtocolDAG", is it possible to force this?

Additional context
Extra question: in your implementation, is the ouput of the solvated leg just the relative hydration free energy? In the publication referred in the user guide, it is mentioned that the two quantities coincide, but I see it leass clearly in the depicted thermodynamic cycle.