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Generally, there's a small difference in speeds:
But we also have to consider the suggested ARM CPU does PCIe 2.1 and we've to add the this detail:
I shouldn't also have a large impact but maybe we should think about it a bit more.
Anyways I do believe this really depends on your use case, if you plan to bifurcate it or not and what devices you're going to have on the other end. For instance for a NAS I would prefer the PCIe 2.1 x 4 as you could have more SATA controllers with their own lanes instead of sharing lanes in PCIe 3.0 using a MUX.
Conclusion: your mileage may vary depending on use case. But I was expecting to have more PCI lanes exposed be it via more m.2 slots or other solution. I guess that when a CPU comes with everything baked in and the board maker "only has" to run wires around better do it properly and expose everything. Why not all SATAs for instance?