“The clause means that the federal government is obligated to ensure the states provide their citizens with a republican form of government.”
Yes, exactly. The clause obligates the federal government, not the states. So only the federal government can fail to live up to that obligation, and thereby violate the clause.
If you can’t understand by now that the clause can be applied by the federal government to rule the compact unconstitutional then I guess no amount of explanation is going to help.