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For MQ, unfortunately we do not control the offering as it's a separate product from Global Mailbox. Our recommendation would be to open an idea request for the MQ team to address in-place upgrades as you have suggested.
For Global Mailbox Cassandra/ZooKeeper upgrades, you should be able to point to the new JDK as part of the upgrade process using Installation Manager. See attached screenshots for an example of upgrading from 6.1.0.1 to 6.1.2.2
I'm also seeing that with MQ 9.3, you will have to install MQExplorer separately.