My understanding of the QPI links is that one of them communicates with the components on the board, and the second one is to communicate with the other processor. That would be a quick and dirty explanation of why the W36xx has one and the X56xx has two. Other than dual-processor ability, the main difference I see in those two is the amount of memory supported, 24GB vs 288GB. If by "I do not intend to overclock" you actually mean you don't intend doing anything outside of the published specifications, then this fact may not be of interest to you: The W3690 in fact supports 48GB, if the board supports it. That's my personal experience as I have a couple of machines with W3690 running at my house, one of them has six 8GB modules installed.
One more question, this time on stepping codes (assuming that you want to match x2 X56xx Xeons on a dual CPU mobo) Is there a way to tell the stepping code 'offline' i.e. just by the serial on the chip? In this example, we have two 'matched' Xeons who do have identical stepping codes and will work as a pair without any issues. As you can see, 6 out of 8 digits of the serial match. Meaning they are probably closely produced in a batch. So can you tell just by that serial? Would Intel provide such info?
Both chips are identical in every way, When you research a cpu to find compatibility, you should use that stepping number on the chip, aka: Chip ID number
Your not going to notice any difference in either. Get a 5600 series if you are going to get a dual board or a 3600 if your going to keep that one. I don't know why you don't want to overclock. I bought a pair of X5675 for my SR-2 board and run them at 4.5ghz 24/7 for a couple years with zero issues. Big difference from 3ghz to 4.5. These cpus can handle it.