I forget who, in the S4 official thread, but they took photos of the 1080 TI mini which appears to use the same cooler, and the Noctua Fans on top were still under the height of the i/o port plate, so I am hoping this works.
As for Noctua, GREAT company. Emailed them about this, at first they said no they are not for sale individually from the cooler and then asked why I wanted them. Explained the build, need for low profile but high static pressure and quiet, and sent them a pic of the S4 case. They responded back positively and were like, lets get you two asap!
So Kudos Noctua!