Here are some reasons:
- M.2 SSD's on the SATA controller is still usually cheaper than the M.2 SSD's on nvme.
- Some people don't know the difference or aren't aware that M.2 only describes the form factor and not the performance and subsequently buy SATA m.2 drives.
- space limitations may restrict some use case from connecting a 2.5" drive and revert to a m.2 form factor. In this case, they may not need the performance gains nvme has to offer, so why put extra $ into something you won't necessarily reap the benefits for.
Personally, I wouldn't waste m.2 space for a SATA drive, but some will for weird niche reasons.
As for your question about Mobo slot configuration. It's a flexibility thing. The 2nd m.2 slot usually shares pci-e lanes to the PCH so you can either connect 2 SATA drives to it using the SATA connectors (usually SATA ports 5, 6), or connect a m.2 sata/nvme ssd to the 2nd slot. This is why you'll see in the mobo user guide that tells you if you connect to the 2nd m.2 slot, SATA 5, 6 cannot be used. So this flexibility of configuration really depends on the motherboard vendor as AMD/Intel typically only prescribes a percentage of the total PCI-E lanes to very specific tasks and leaves the motherboard vendors to decide what they want to include on the motherboard.