Part of the Hong Kong situation is that locals have grown to resent the increasing presence of mainlanders (as individuals or corporations) in their workforce, business world, and intelligentsia. However, this was inevitable, just as with LA and New York becoming nexuses for American migrants as well as for strivers from across the world. While the Party will tend to bring Hong Kong's internal policies more in line with their broad plans (for instance, Xi Jinping has been centralizing power from regions across China during his office), Hong Kong is a relatively profitable and consolidated entity, as well as a good test case for whatever trend the party might want to investigate at a given moment, so there isn't much impetus to radically transform the governance or economy of the region. Sure, maybe mainlanders and mainland business will continue become a stronger lobby as they become a larger proportion of the population or gain more control of property and enterprise, but that's more of a sociological question.
One contentious issue over (quasi-)reunification for Taiwan would be what happens with the Taiwanese military; the United States has some interest in that aspect too given its history with military aid to Taiwan. However, even the Pentagon hawks have come to terms with Taiwan Finlandizing as a minimum in the future (apologies for all the coarse political coinages).
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