I think that makes it a non-standard implementation though (I agree it's certainly more practical for the user), sounds like it's usb-c pd but with nerfed data, an odd choice that feels like it would actually have cost more to develop than just adding two identical usb-c 3.x ports...

Why would it be non-standard? USB-PD is almost completely decoupled from the rest of USB, and USB-C connector doesn't imply 'super speed' lanes are available. The only thing it really changes from an implementation perspective is that you don't have to route high speed lanes to the port, and don't need them to be available on your USB controller.

Doesn't seem to be very Apple-like to have two identical looking ports with different function, though.

I suspect the limitation is that the SOC doesn't have the IO bandwidth to support two ports at usb 3 speeds (remembering that the SOC was designed for iphones which physically only have one port).

I'm not sure exactly what the USB specs require, but there are a lot of phones out there that only support USB 2.0 data speed but do implement the current fast charging protocols. It's absolutely a mainstream thing.