It is true that you won't be able to boot from micro-SD if the SPI ROM doesn't transfer boot, which is what's happening to you.
I haven't had to do this, but I expect you could short the appropriate pins on the SPI ROM chip so that it doesn't boot and boot to micro-sd (or eMMC). Otherwise yes, you'll have to to the mask ROM mode thing.
The only reason I mention DietPi is that I know it works. I found out the hard way that all the bootable micro-sd cards I made did not actually boot with a blank eMMC. So I went to the wiki and tried various images, and DietPi was the first one that worked. I was able to use that to zero the eMMC and then write U-boot and NetBSD to it. So if I were you, I'd put that DietPi micro-SD in, and short the appropriate pins on the SPI ROM. When the boot process starts, you can remove your short. Once booted, immediately zero the SPI ROM.
I haven't had to do this, but I expect you could short the appropriate pins on the SPI ROM chip so that it doesn't boot and boot to micro-sd (or eMMC). Otherwise yes, you'll have to to the mask ROM mode thing.
The only reason I mention DietPi is that I know it works. I found out the hard way that all the bootable micro-sd cards I made did not actually boot with a blank eMMC. So I went to the wiki and tried various images, and DietPi was the first one that worked. I was able to use that to zero the eMMC and then write U-boot and NetBSD to it. So if I were you, I'd put that DietPi micro-SD in, and short the appropriate pins on the SPI ROM. When the boot process starts, you can remove your short. Once booted, immediately zero the SPI ROM.