You seem to be asking multiple unrelated things, which would be better addressed in individual threads.
Questions about how to format a MOBI/AZW3 for a specific look are best addressed in our
Kindle Formats subforum, not this one (which deals primarily with the devices themselves).
As for registering, mostly what you lose is collections (unless you are jailbroken).
You also lose inside-the-book Wikipedia lookups, IIRC.