This is true in one sense, but also misleading. Here's a little more detail on the 4,1 and 5,1 PCIe configuration.I have a Mac Pro 5,1 and tried different card slots for my old SSD adapter. They were all the same... according to Apple, the Mac Pro 5,1 slots are all the same speed.
Slot 1 and slot 2 are PCie 2.0 x16, and each has an independent path into the CPUs and memory controller. With an up to date boot ROM, each of these slots should operate at 5GT/s with any card that's capable of it, and potentially give you ~10GB/s of bandwidth.
So these are the high performance slots. Notice, though, that to take full advantage of them you must use a card with an x16 PCie bus width, and that actually uses all 16 lanes. If you have a card with a narrower bus width (x8, x4, x2, or x1), you will get correspondingly reduced performance.
Slots 3 and 4 are PCie 2.0 x4, and, critically, share an x4 connection to the CPUs and memory controller, through a PCIe switch. With an up to date boot ROM, each of these slots should again operate at 5GT/s with any card that's capable of it, and potentially give you ~2.5GB/s of bandwidth, as long as you're only using one of the two slots. If you're using both Slot 3 and Slot 4, the available transfers/s and bandwidth will be split between them.
So these are the lower performance slots. And similarly to the above, to take full advantage of them you must use a card with an x4 PCie bus width. If you have a card with a narrower bus width ( x2 or x1) you will get correspondingly reduced performance.
Perhaps obviously, there's more to this than just what I described here - there are a number of other limits that could pop up in different circumstances, particularly in situations that create many small bus transactions rather than fewer large ones. But the hardware configuration limits above give you a good basic starting point.