We don't actually import anything or rename anything in the AddOn\Create command. All we do is give you the option to export the data if data exists. What will attempt to rename stuff, though is the 2.0.0 Alpha setup class, and we currently suspect that's what you're seeing.
Check out XF\Install\Upgrade\Version2000010::step24().
There's a slight margin of error when it comes to option title phrases:
PHP:
'option_([a-zA-Z0-9]+)' => 'option.*',
Presumably the option phrases you saw that didn't get renamed may have had IDs that didn't match that pattern. The pattern is fairly strict, but deliberately so as to avoid false positives.
On that basis, I think we're safe to call this as designed right now.