Hi,
The LPC546xx has on-chip flash which can save code and data and you can run code in on-chip flash directly, I do not know why you need to connect spi flash to save code.
Anyway, I agree with you that you can not use on-chip ROM bootloader if you want to connect external SPI flash and save the code in external spi flash. In bootloader mode, FC3 is configured as spi slave mode, so that external host spi in master mode can write image to on-chip flash of LPC546xx.
FC3_SCK PIO0_0
FC3_SSELO PIO0_1
FC3_MISO PIO0_2
FC3_MOSI PIO0_3
If you do want to connect external spi flash, you can develop a second bootloader, after Reset, the second bootloader is run, in the bootloader, you can set the spi in master mode, read code and data from the spi flash to internal SRAM, and run in internal RAM.
Hope it can help you
BR
Xiangjun Rong