I've worked with a fair number of Java APIs. I would put the quality of their Java SDK in the bottom 10%. It has the stench of really old Java. Remember how the first Java APIs reeked of C? The fact that the PayPal Java SDK still looked like hastily ported C code in 2011 when I last worked with it makes me worry that their entire manner of using Java is stuck in the early 2000s. That's being generous. It's the kind of Java you'd expect to see written by a company that still thinks about "applets" and "beans" and tries to come up with clever coffee double-entendres for their package names.
My theory: PayPal is big but they know they are vulnerable. They've acquired BrainTree and that helps. I suspect they want to improve their technical chops and felt a need to migrate away from Java in order to break free of their organizational quagmire. PayPal is from 1998 and if their Java SDK is any indicator, they probably have a Subversion commit log for their core systems going all the way back.
This sort of move is the kind of thing I could see myself doing if I were in a decision-making position at PayPal. Attempting to invigorate sensible modern Java practices within that organization would seem hopeless. I would have to start anew with an approach that is free of poisonous legacy.
As others have pointed out, the fact that a rewrite yielded so little performance gain is decidedly troubling. At least they got a fun and well-linked blog entry out of it. If I had just gone through that effort and reaped such a modest improvement, I'd be crestfallen.