I don't know all the answers to your questions/speculations, but considering that Patek's complicated watches are not assembly-line pieces and there is often a wait to get complicated pieces through ADs--in other words, it's much more of a made-to-order piece--I suspect that the rarity of the 5050 reflects the fact that there was low demand for it while it was offered by Patek.
The sheer supply of the 5059 makes me think that it's indeed a very popular piece, though not difficult to obtain. If it wasn't popular, why would Patek be making so many? Companies often estimate demand incorrectly, but I doubt you'll see Patek making 1,000 perpetual calendars and hoping they sell. The bigger sellers, generally speaking, will be produced in higher quantities. Of course, other factors come into play such as limited watchmaker expertise (and limited watchmakers) and movement supply limitations as in the case of the 5970, both of which may contribute to its relative scarcity (but even the 5970 can be readily found on the grey market if you're willing to pay the freight and accept the attendant risks).
I don't think this is a new concept in the art world. Tepid initial market response leads to rarity which itself sometimes leads to desire, a hot item and high prices. It is a shame because market participants are ostensibly reacting to rarity and price rather than an understanding and appreciation of the values and work of the artist as embodied in the piece of art.