I checked the launch of EFI\Grub mode when placing the entire system on NVMe, everything starts up and works fine with NVMe (while the SD card is used exclusively for u-boot placement, because I have not yet checked how my u-boot can be written to SPI). At the same time, the device startup sequence works correctly with my u-boot (unlike the stupid option used in the official u-boot for NVMe) - if you connect an SD card, the system automatically starts from the SD card, the system on NVMe does not interfere with this in any way, and I assume that the RKTools tools for work via USB, the same will work correctly. 
p.s. I’m not really worried about where I’ll have a u-boot, on SPI or on an SD card, and I don’t want to risk my instance to waste time on recovery later if something doesn’t work. If someone wants to check how the new u-boot works from SPI, it can be installed on SPI by the standard procedure from armbian-conf (all files are included in the image).