Boot sequencer serves a different purpose. It runs before the core starts. Booting from an eSPI flash, the core has to be configured correctly and starts the Boot-ROM code on-chip. It runs after the boot sequencer if any. So you can enable eSPI FLASH if boot sequencer has done all the necessary configurations. Also, the configurations in an eSPI FLASH will overwrite any memory mapped registers.
When you configure pins CPPARBx[SELn]=11 and CPDIRxB[DIRn] = 11, it will configure PB20 as SPI_SEL function.