My biggest confusion is about the physical connectors and their importance.
For instance the Sabrent 4 disk card has a physical x4 connector that can be placed in a x4 x8 or x16 slot and is said in this forum to be able to reach 3000 MB/sec.
Two different thing: electrical connection and physical connection.
The Power Mac has four x16 physical slots but only two of them are electrical x16 slots. The other two slots are electrically x4 slots.
x4, x8, x16 are link widths indicating the number of lanes. A x16 slot can connect PCIe cards with x16, x8, x4, x2, or x1 lanes (electrically and physically).
x4 can achieve 3000 MB/s only if the slot is PCIe 3.0, or gen 3, or 8 GT/s. Those are different ways to indicate the link rate per lane.
The MacPro4,1, and MacPro5,1 is limited to PCIe gen 2 link rate (5 GT/s).
The MacPro1,1 and MacPro2,1 is limited to gen 1 (2.5 GT/s).
The MacPro3,1 has two x16 gen 2 slots and two x4 gen 1 slots. The x4 slots can connect PCIe cards with x4 or x1 lanes. A PCIe card with x2 lanes will connect as x1.
You can connect PCIe cards that are physically narrower than the slot.
You can connect PCIe cards that are physically wider than the slot by using a riser.
The Ceacent ANM24PE16 has a physical x16 connector and can only be run in a x16 slot.
It can work in a physical x16 slot. The slot could be electrically x1, x4, x8, or x16.
It can work in a physical smaller slot using a riser adapter or cable.
Having a look on the pics it's clear that there are 2x16 pins connected.
Are you counting metals pins on the card? Don't do that. All PCIe cards of the same physical connection size usually have the same number of pins. A PCIe lane consists of 4 pins, two on each side of the PCB. A PCIe lane is a bidirectional link using differential signalling (transmit and receive, + and - ).
Maybe you are talking about the number of surface mount components (resisters?) next to the pins. I think that is an indication of the number of physical lanes that are electrically connected. You can usually look at a picture of a PCIe card to see if all the physical lanes are electrically connected.
Another card (unbranded) has a physical x16 connector and is supposed to run in a x16 slot. This card has 2x8 connections which is half of the lenght of the physical connector.
Yup that is definitely an x16 physical card with x8 electrical lanes. It uses the ASMedia ASM2824 which supports PCIe gen 3 x8 upstream connection.
https://www.asmedia.com.tw/product/249yq0aSx7zRFGJ9/7c5YQ79xz8urEGr1
Is there just different ways of "wiring" the cards or do the differ in terms of disks sharing the same lanes which would mean slower performance. Does it impact speed per individual disk etc?
The ASMedia ASM2824 is a PCIe switch. It supports gen 3 and 24 lanes total. The upstream is limited to 8 lanes which leaves 16 lanes for downstream devices. In this case, there are four downstream M.2 slots. An M.2 slot can have up to 4 PCIe lanes so 16 downstream lanes is exactly enough for that.
A PCIe gen 3 switch can convert the fast and narrow gen 3 x4 of the NVMe device connected to the M.2 slot to the slow and wide gen 2 x8 of the Mac Pro without much loss in performance.
upstream: 5 GT/s per lane x 8 lanes x 5b/10T = 32 Gbps.
one downstream device: 8 GT/s per lane x 4 lanes x 128b/130T = 31.5 Gbps.
In this setup, you have 126 Gbps on the downstream side of the bridge and 32 Gbps on the upstream side of the bridge. It's like a USB 3.x hub. All the downstream USB 3.x devices can perform at max speed but if more than one tries to transmit or receive at the same time, then they will get limited by the bandwidth of the upstream connection.
Lastly does it matter at all in these older beasts or would it be important to consider these specs to get the most out of the read/write performance of the disks?
To get the most out of your gen 2 x16 slot, you would use a gen 4 x16 PCIe card.
upstream: 5 GT/s per lane x 16 lanes x 5b/10T = 64 Gbps.
one downstream device: 16 GT/s per lane x 4 lanes x 128b/130T = 63 Gbps.
A gen 5 x16 PCIe card could be slightly faster then a gen 4 PCIe card but would not be worth the expense since you will be hitting the upstream limit.
64 Gbps is 8000 MB/s but in general you can only get ≈75% to 85% of that as actual data ≈6000 MB/s .. 6800 MB/s. The rest is overhead and inefficiencies.
If you are only connecting gen 3 NVMe devices, then a gen 3 x16 PCIe card is sufficient. A gen 3 x8 PCIe card is alright if you're not doing RAID 0 or won't be transmitting to or from multiple NVMe devices at the same time.
Note that PCIe has separate lanes for transmit and receive, so you should be able to transmit 6000 MB/s while receiving 6000 MB/s at the same time.