Gosh, it would be so efficient if default approval of a merge would give us the ability to merge other duplicate family members, but that's not the way it works.
I think you must be reading the language at Help:Merging that says "While confirming a merge you may be prompted to merge or match the fathers and mothers of the two profiles." That wording seems a bit misleading. When you merge a pair of profiles that have different profiles for the parents, you are asked to reconcile the discrepancy in the parents (I don't recall the exact wording), but if you see need for a merge, you have to do through the standard merge-proposal process, one profile at a time. Note that the next sentences on Help:Merging say: "On WikiTree we don't merge trees, we merge individual profiles. This can be time-consuming but it gives you the maximum amount of control."
If you are working with a family group whose Trusted List members aren't responding to merge requests, considering submitting Trusted List requests for the family member's profiles -- and in your request indicate the whole list of the same managers' profiles that you are interested in. If the profile managers don't respond in a reasonable time, see the procedures at
https://www.wikitree.com/wiki/Help:Unresponsive_Profile_Managers