Short answer: no. The BootROM on the MT7988 is fairly similar to what was already in MT7986 and doesn't support booting from NVMe directly.
However, you could go ahead and implement PCIe support in U-Boot -- then you can have TF-A and U-Boot sitting on SPI-NAND or SPI-NOR and have it do UEFI standard boot from the NVMe to load a generic purpose OS.
At this time the only missing thing is porting the PCIe driver from Linux to U-Boot, so it's purely a software limititation.
You are probably referring to the image format (uImage.FIT incl. squash rootfs) used by OpenWrt on the R3 (and many other systems which can support that). And yes, as the R4 is yet another board where we can implement validation of the root filesystem by the bootloader, that's what's going to happen for the official OpenWrt image.
If, for what ever reason, you are not happy with that it's easy to tell the kernel to use something else as rootfs (such as an additional ext4 partition you may create) by using the root= kernel cmdline parameter set in the bootargs variable in U-Boot.