We're not marking up the exchange rate. 0.5% is the only fee.
http://www.bloombergview.com/articles/2014-11-12/banks-manip...
http://www.bloombergview.com/articles/2015-02-09/banks-will-...
And that's just from the last three months, in an arena that is already heavily regulated by the SEC.
I am a huge fan of Matt Levine's work, but the articles you reference are about banks who participate in the FX markets, which is... different.
(Relevant disclosure: I work at Stripe.)