However, both with Kickstart 3.1 and 3.X, NetBSD cannot boot from CF connected to primary slot of FastATA; "insert FD animation" appears on screen. I can boot from this CF if it is directly connected to internal IDE slot without FastATA. I know almost nothing about Amiga, and I don't know whether it is possible, in principle, to boot from disks connected to FastATA.
The boot code for certain controllers doesn't support booting with NetBSD bootblocks even though they'll boot AmigaDOS just fine. This is the case with my Blizzard 1260' SCSI interface, for instance.
If direct booting really doesn't work for FastATA, you can either boot directly from the regular IDE, or you can boot in to AmigaDOS and use loadbsd to boot.
My CF card is 8GB size, and root partition of NetBSD is larger than 4GB. Is this related?
That shouldn't be an issue at all. After all, you're not seeing the bootblock loading and prompting you for the kernel name and options, right?
John