Unless the one it comes with isn't as fast as the one you want, or they didn't integrate one at all, or you need more than one.
> Across all desktop PCs, the most common number of slots filled is one (a single GPU), and the average is surely less than one (systems using zero slots and relying on integrated graphics must greatly outnumber systems using more than one slot).
There is an advantage in having an empty slot because then you can put something in it.
Your SSD gets full, do you want to buy one which is twice as big and then pay twice as much and screw around transferring everything, or do you want to just add a second one? But then you need an empty slot.
You bought a machine with an iGPU and the CPU is fine but the iGPU isn't cutting it anymore. Easy to add a discrete GPU if you have somewhere to put it.
The time has come to replace your machine. Now you have to transfer your 10TB of junk once. You don't need 100Gbps ethernet 99% of the time, but using the builtin gigabit ethernet for this is more than 24 hours of waiting. A pair of 100Gbps cards cuts that >24 hours down to ~15 minutes. If the old and new machines have an empty slot.
He's not advocating from removing PCIe slots, but in practice, it's needed by way less consumers than before. There's probably more computers being sold right now without any PCIe slot than there are with more than 1.
Discrete GPUs generally consume two PCI slots, not three, and even the mATX form factor allows for four PCI slots (ATX is seven), which gives board makers an obvious thing to do. Put one x16 slot at the top and the other(s) lower down and use the space immediately under the top x16 slot for an x1 slot which is less inconvenient to block or M.2 slot which can be used even if there is a GPU hanging over it. This configuration is currently very common.
It also makes sense to put one of the x16 slots at the very bottom because it can either be used for a fast single height card (>1Gb network or storage controller) or a GPU in a chassis with space below the board (e.g. mATX board in ATX chassis) without blocking another slot.