If Person A performs a merge and spends some time QAing, without checking the result in, it will not affect in any way to Person B. Impossible.
If Person A performs the merge and then he checks the changes in, Person B might face a merge operation if his changes are basing from a previous changeset and they are in conflict with the changes done at the merged changeset. If Person B changes are not in conflict with the ones merged then Person B can just update-merge, Plastic will let you do it: Update-Merge Dialog
Then you mentioned the "there is a pending merge" dialog, this dialog will only will be displayed when you start a merge operation, you don't finish it and finally you try to check-in the partial operation result. Once you face this scenario you should repeat the merge in order to continue with the unmerged candidates and finish the operation, then Plastic will let you check the merge in.
Finally, answering your question:
What is sent to PlasticSCM server in-between merge and replicate that
affects other users, and why?
I'm afraid nothing. If you start a merge at the central repository or the distributed repository it won't affect third party users working with replicated repositories, they are completely independent until you push the merged changeset to external repositories.