Does this wastegate have a "fire ring" or valve seat? The lipped edge side should fit the fire ring and seal it. The 2nd picture where you see no edge should be welded to the manifold.
Ok lemme edit that, from what I am seeing you have two flanges right now? The wastegate has a flange that mounts to the valve seat side, and then you have a second flange for the dumptube? Play with the assembly of the wastegate to the flange and see if the fire ring fits into the groove, if so then that side is meant to bolt to the wastegate.
Here is a diagram of the two F41 flanges:
My PTE wastegate is v-banded, but the 2nd flange they included for the dump tube has a lip inside of it that allowed the dump tube to slip into the groove easily for welding. This could be what the lipped edge side of the flange was meant for.