Uh, no. While it's true that SD cards offer backwards compatibility with MMC, modern cards transfer using a 4 bit wide parallel bus, and it's not nearly as simple as the SPI mode. With regard to your argument, have you ever looked at the flash chips in an SD card? Last I checked, they use the same memory dies as the "embedded" packages, and add the cost of an SD controller and more complex packaging. On the host side, there's the cost of an SD controller (although that's probably "free" with the SoC) and socket.
More specific to the original point, if a phone already has 16G of flash, the cost of upping it to 64G is minor - the parallel interface you mention is already there, and the difference in packaging costs between 16G and 64G chips is likely zero.