Forget about “Reference boot.ini”. Don’t change anything, just burn selected (latest) Android image (with Etcher) and install it; turn N2 off, remove any uSD card, attach eMMC module take care that SPI switch is on the right (eMMC) position and power on N2. Installation should start and finish without a problem. IIRC after the initial setup you have to turn N2 off and on to boot Android.
6. 7. 8. are separate topics and can be discussed when you have both systems (CE on uSD & Android on eMMC) up and running…
Simplest way to dual boot is: boot to CE with both uSD and eMMC inserted, and boot to Android when uSD is not inserted. There is another way (using SPI switch) but that takes more preparations…