First of all, I know about this:
How does it boot?
You have to boot from SD but a USB HD can “take over” after the initial boot. You cannot boot without an SD card.
This is true, in case of Raspberry Pi we can't boot without SD card. For most users SD card is ideal boot source I think.
I have to create my custom PCB board based on BCM2835 which is 99.9% same as RPi, because I need more robust hardware design to be vibration tolerant (and also some other task-specific modification).
AFAIK SDIO interface is same as SPI interface, so I suppose I can use small SPI Flash/DataFlash IC chip as boot source. Could I do so?
Yes, flashing of memory IC in such case is a some sort of pain but it's acceptable. I hope I can use some jumpers to flash it outside.
Unfortunately I can't learn about this from available BCM2835-ARM-Peripherals.pdf datasheet, it looks like very cut and incomplete in comparison to other manufacturers.