The use of a OEM modified PCIe connectors are no different to the mining days where our risers used a non standard USB connector to provide the required power and data lines, use those cables in a standard USB slot and you will potentially have a bad day. Some OEM’s have chosen to use non standard PCIe slots to expose PCIe lanes for various reasons, HP, Dell and ASUS server class kit spring to mind (eg that’s what I tend to encounter), I am sure other OEM’s will have done similar, but the clue with a non standard interface is the non standard part, it kind of gives the game away.
Other general exceptions to the PCIe standard do exist, the SMBUS pins for example are normally not used on consumer grade boards, so they aren’t connected by many OEM’s, but over the years a number of Dell (Broadcom) fiber cards, the Sun F20 NAND accelerators, early HBA’s (Broadcom) and even Nvidia 50 series GPU’s have had a hissy fit when it finds they are connected, but those are widely known and documented, as is the fix: a tiny bit of Kapton tape over pins 5 & 6.
Then let’s look at BIOS implementation, most consumer OEM’s didn’t bother to enable rebar despite it being part of the PCIe standard for many years. Then AMD couldn’t stop saying it so often that OEM’s enabled it for the most part. We’ve also seen various BIOS updates to improve timing accuracy with NVMe, again less to do with ‘the standard’ and again more to do with the OEM’s producing hardware for it needing the goal posts moved slightly.
So yes, any PCIe compliant card is backwards compatible with earlier standards of PCIe, that’s one of the basic principals of PCIe standard. No you can’t fit a bespoke OEM custom PCIe card into a PCIe slot without a suitable adapter (Ali-Exlress sells some weird custom to standard adapters), and per the examples provided, some OEM’s can and do interpret the standard with a certain level of latitude that sometimes requires intervention, though often not by the OEM who caused the issue (motherboard manufacturers are often required to push BIOS fixes for other OEM’s stupidity).