So as you all have kindly pointed out, the large sd form factor dev board made by Atmel is less than ideal for use in a HAT which is supposed to help cut down on bulk. I completely understand this. I've come up with a rough schematic and board layout for a WILC1000 based WiFi hat.
There are some major stability issues I am still trying to work out, in that the entire interface goes down after the throughput reaches a certain threshold (around 10Mb/s). I am pretty sure it's a power related issue, the chip probably needs more current than the 3v3 rail can provide. My Pi doesn't want to stay powered on when I try to measure current draw of the card which is an issue.