All you need to do is make sure the dual-MOBI is converted
with the title initially set to your desired title.
The problem is updating an existing dual-MOBI.
Kindlegen won't update the metadata in an existing file at all -- it is a converter only, so you'd have to convert from an EPUB that was saved with the right plugboard. You could do that with calibre's ebook-convert too.
The problem is doing automated conversions in the calibre GUI when plugboards only apply during export.
...
This is a bug, it is just not a high-priority one so no one has really bothered to fix it (and/or spend the time to test it). You generally should use MOBI or AZW3 on its own, dual-MOBI is not a very popular output format.
It basically only affects people who both use plugboards, and send dual-MOBI to Amazon's Personal Documents service (in order to make sure their AZW3-supporting devices get an AZW3 delivered to them).
The intersection of those two groups is not a very large group. And Kovid says the solution is fiddly and also would need testing -- by someone who actually uses dual-MOBI -- to make sure nothing breaks horribly. So it isn't worth the time for him to figure out how to implement it given how few people would benefit.