To me those look like the flange on the hatch cover. I would install it the same way (with a hatch or window kit).
Put some sealant on the bottom, drill holes in it + roof (probably about 6 per corner piece), screw down and dicor over everything.
I wouldn't rely on the TPO roof holding anything down...its just a loose membrane--it would be like securing something to your awning fabric.
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