Well, their SSDs are not PCI-e devices, they are directly connected to the SoC. I think that their use of NVMe is just a compatibility stop gap, they will probably move to a custom direct-access interface in the near future.
They're using NVMe with customizations because NVMe is a good standard. There's no reason to reinvent it from scratch when it works; they can just make the non-standard changes they feel like making, as they have already done.
There's no fundamental reason why NVMe has to be tied to PCIe; it just happens to be that way on existing devices.
