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File a small slit in the end of the slot so the card fits into it, but runs past the back. The card will run at Gen 3 x1 speed, but otherwise work properly.
Many motherboards even come with the end of the PCIe slots open for this exact purpose.
Edit: Gen 3 x1 runs at almost a full GB/s, so a 2.5Gb/s card (notice the change in size of the "B") should have more than enough bandwidth on Gen 3 x1, even at 2.5Gb/s full duplex.
A word of caution for anyone cutting out the slot: make sure there aren't other instructions, like capacitors, ICs, and NVMe drives in the way of where the PCIe card will be.
The manufacturers that have the slot pre-cut will have already reserved the space, but even then, it's on you to check that it's suitable for a x16 if they only reserved space for a x8 card.
I'll likely go for a 4 or 6 gigabit port card, so PCIe gen 3 x1 is not a problem. Am I correct in understanding that the card will run at PCIe gen 3 X1 if I do this?
What can I do if the card is PCIe gen 2 x8? These cards from Silicom are really cheap on ebay
Correct. The situation you described in the original post would result in Gen 3 x1 speeds.
The interface will always default to the fastest standard that both sides can support. If one is gen 2 and the other is gen 4, gen 2 is the highest that can be supported. If one side is x8 and the other is x4, x4 is the highest that can be supported.
If you put a Gen 2 x8 card in a Gen 4 x1 slot, you will get a Gen 2 x1 link.
Alright thanks