Hi Steve,
My panniers are 41 liters.
I can open mine because I mounted the top box like that, "the long way". To do that, I cut a chunk of the Adv seat. I don't think you need to do anything if you just remove the pillion seat on a standard GS.
If you mount it like it is in the second pic, you need to rise the top box about 50mm to get the lids of the panniers. At least on a GSA, I'm not sure about the rack height on your GS.
You can ask Uncle Albert maybe, he's got the Zega XL mounted on his GS.
Cheers,
Michel