I think you are overestimating the value of defaults, whose purpose is to enforce the greatest
common denominator. You'd be surprised how many people still have a Kindle Keyboard (and haven't upgraded the firmware on it). Usability is king.
Nice fancy words though.
Also, side note: I despise Macbooks, and this (deprecation of useful functionality) is only one of the many reasons. Great example.
In the real world, enforcing highfalutin standards regardless of what people actually need, is one reason Macs will never catch on... and why I doubt the calibre defaults will change just on your say so.
Hopefully the conversion bug can be fixed (not that it reflects badly on the format itself, simply because a bug only affects the legacy format).