To elaborate: calibre does not have the ability to update the metadata within the AZW3 component of an existing dual-MOBI (type "both"). This is due to the difficulty of robustly modifying the metadata headers in a dual-MOBI.
Kovid hasn't devoted the time to fix this, since it basically only affects people who email to their Kindle and want to receive AZW3 via the PDOC service. Which is a very small percentage of users, and it is simply not worth investing the time it would take to create and test a fix.
So you will probably just have to live with setting the desired title metadata during the initial conversion to dual-MOBI. Or use old MOBI.
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