[1] http://clover-developers.blogspot.com/2014/09/apple-pay.html
Just a guess! but it would avoid some pretty massive technical hurdles to international acceptance.
But yeah, they obviously found a way to implement ApplePay - hell, Apple probably did it for them.
Banks generally hate anything that takes away their branding. Less sleek of this -- i.e. reprogrammable Visa cards -- have been around for a few years but banks never supported them, again because of branding.
I also am not certain that Apple Pay "massively encourages" a single default card. It looked quite easy in the demo to display multiple cards and switch between them. Looked easier than taking a card out of a crowded wallet and putting it back in, actually.
Also there are some practical in RL issues that come up with most NFC payment readers (namely a lot of the installed readers have short range, and awkward pad placement) which makes non default much less attractive.
As for the display issue, the issuers concern is that they are pretty limited as far as making things distinct. I mean hell, every card company is going to have black cards. There are no sideways cards, no premium materials, no metallics, etc. They have a relatively small image, which has to still look good even if cropped to lose the bottom 80%. Basically they get space for bank logo, card logo, and a non distracting background.
So if they are willing to give up on all that and a fee, it doesn't seem all that out of the question for them to allow their logos to be used on a flexible card, and (presumably) not pay a fee.