[SepTop & ABFEs] clean up equil settings output indices so that it enforces 'all'

[IAlibay]

See: https://github.com/OpenFreeEnergy/openfe/pull/1057/files#r2166457778

[hannahbaumann]

@IAlibay I switched the raising of the error in the protocol to a pydantic validator in the settings, would this also work for ABFEs? Or do you see cases where we wouldn't want to fail this early?
See this commit: a2aa81e