The "SD Specifications Part 1 Physical Layer Simplified Specification Version 2.00" states on page 93:
The SPI standard defines the physical link only, and not the complete data transfer protocol. The SD Memory Card SPI implementation uses a subset of the SD Memory Card protocol and command set.
What does it mean by "physical link only"?
When it says that SPI will only support part of the SD memory card protocol, what part is it that is not supported?