When altering a user's groups, I need to be able to replace their group if they are already in the same group in a PEX rank-ladder, as opposed to adding an additional group.

Also, within my plugin, when a command accepts a GroupName as a parameter, I need to verify whether that group is within a given rank-ladder. For instance, if the command is only targted at members, it needs to only allow groups that have the rank-ladder: Members. If the command is targeted at staff, it needs to only allow groups that have the rank-ladder: Staff.

How can I get a list of groups that only belong to a given rank-ladder?

This is very specific functionality for PEX, you should be linking PEX if your plugin requires PEX-only features.