For kindlegen problem, maybe read from
this post to #86. No idea if KCC still uses Python's TKinter for GUI, I think it changed to QT?
Also double check that you've downloaded kindlegen for Mac
A for old mobi vs azw3 dilemma you should probably stick to azw3, there is no harm in using newer format and not using most of the newer formatting. Panel View is not the only reason KCC uses newer Kindle format.. there was something about better fullscreen viewing and support for higher quality images.
@Doitsu: Just checked, you're right. JMMM doesn't correctly change title or author for dual mobi files. And since the python script doesn't offer editing full set off metadata fields there is still need for Calibre to update it metadata editing. If it can produce dual mobi files it should also be able to correctly change metadata for those files. Lots of people who are using Amazon Cloud for personal documents/sideloaded books are generating dual mobi and sending them because they want to get KF8/azw3 file on their Kindles. Even more people use metadata plugboards for inserting things like series into book title... So some people are bound to use both
: D