Walt has been spot on with all the right answers to this imo. I have no intention of adding more preferences at the moment, it will only add to the confusion about what gets used when.
Right now it is as simple as I think it can be - a user who has only one format for a book, will get a count of pages in that book as the result of converting it to ePub, assuming it wasn't an ePub to begin with. The special case exemptions to that are PDF, CBR and CBZ formats - in those circumstances for page counting it does no conversion and handles each with some format specific algorithms. Though if you had other statistics turned on like word counts then it would still attempt a conversion.
If you have multiple formats for a book, it uses your preferred input order to decide which to convert to ePub. Most people will (sensibly) leave it at the calibre default of ePub at the top - there is *no better* format to convert from than this. MOBI is not special cased, it just usually sits as second on the list on most people's systems, and converts very quickly/well to ePub.
Putting another format at the top of your preferred input list like RTF really doesn't make any sense to most people or in most circumstances, so I don't intend to complicate this all further with yet another preference for it.