I think it should be pointed out here whilst "pitch" has standards (by definition) connectors often don't. Molex, Amphenol, Harwin, Samtec etc.. will have a variety of IDC 2mm connectors that may or may not be compatible with other manufacturers shrouded headers. It's a pain having to source specific connectors, but the fact that most 0.1" shrouded headers are mostly compatible with each other is mostly just co-incidence. This isn't the case for many other types of connectors.
It is one of those gotchas that just happens - never assume something has a generic connector, or that a specific pitch means it will be compatible with any connector of that pitch.
I'm sure Xilinx had good reason to use such a connector - even if it is to increase sales of any "custom" adapter cables.
As an ex-designer still working for one of those aforementioned connector manufacturers, I'll just throw a bit of additional information in here. If you know all this already, feel free to stop reading, this is for those less familiar with the connector industry.
2mm pitch "standard" pin headers (as shown in Gerhard_dk4xp's post) typically have a 0.5mm square pin, and that, as far as I've seen, is pretty universal for this pitch of square pin header. Mating cable connectors for discrete wires would easily fit in the hole supplied in the Xilinx box, as they are pretty much "on-pitch" for their length (2 pins per row = 4mm long, etc).
The fun comes with IDC. Because the rear fixing bar needs to latch down outside the main housing, it significantly increases the length of the connector - and there's no conformity for this length, unless there is an actual Standard it conforms to. Many moons ago we used to sell a 2mm pitch IDC, and it wasn't designed to any particular Standard and therefore did not necessarily fit in a competitor's shrouded header. BTW, we don't make 2mm IDC sockets anymore, only 1.27mm pitch, and we only guarantee a fit with our own mating latched shrouded headers, we've not tested it with the rest of the options out there.
So, I guess Xilinx have chosen a slightly more compact IDC from all the options out there, and some of the bigger ones don't fit. But I bet a discrete wire one will fit without any issues, as I bet they are 0.5mm square pins.
Lesson over, sorry can't help myself sometimes!