First of all, yes that should work.
I noted that, while the specs explicitly say "PCI Express 2.0 x16", the Hardware Maintenance Manual calls it a "PCI Express x16 graphics slot" (emphasis mine).
I have seen this a lot. Usually that means that the writer of the manual has no clue about the hardware he or she is describing. A "PCI Express x16 slot" simply is a "PCI Express x16 slot". You should be able to connect any PCI-e card to it. graphics, network, RAID, ... whatever.
I suspect that this erroneous description started because in most cases a PCI-e x16 slot is used to upgrade the graphics, followed up by lazy copy-writing.
Does this mean that Lenovo deliberately prevents cards other than graphics cards from being recognized in this slot?
They should not. If they do then their design is broken and you should take the computer back to the shop and return it.
Having said that, I have run into the following problems before:
- A Compaq PC (P3 era, no idea which model it was) not booting with some PCI cards which worked perfectly in other desktops.
- A trio of Dell Optiplexes disabling their onboard graphics when a card was present in their sole PCIe slot (which happened to be a RAID card, leaving me with no graphics at all).
- Several laptops with mini-PCIe slots which only recognize a select few cards.
This means there are at least several systems out there which do not follow spec and which should be considered broken and ripe for a trashcan.
But before you talk the Thinkcenter back, make sure that the card(s) work in other computers. They almost certainly will, but it is best to be safe. (Despite the changes of having two broken PCIe cards is rather slim).