Settings objects should not allow invalid options

Describe the bug

The SepTop/ABFE protocols expose some user options which are hard to configure (they are coupled to other values like the n_replicas) or only have a single allowed value (like the output selection index for the restraint generation ). These both create a poor user experience where they fail during protocol creation when they should fail early, this could be while configuring the settings, creating the protocol with the configured settings or in the validation method while making a transformation.

To Reproduce
Steps to reproduce the behavior (ideally a minimally reproducible example):

Software versions

• Which operating system and version did you use? (e.g. ubuntu 22.04.5)
• Which method did you use to install this package? (e.g. conda-forge)
• Copy/paste the output of conda list (or the equivalent for your package manager):

Output

Expected behavior

Additional context

Start by reviewing the SepTop and ABFE settings objects and the protocol creation and validation paths described in the issue. Identify options coupled to n_replicas and the restraint-generation selection index, then verify that invalid configurations fail at settings, protocol creation, or transformation validation rather than later.