That may be a FreeBSD limitation. I think that the entire partition is read into memory by that tiny FreeBSD bootloader.
The problem is worked around very easily by simple use of math. Let FreeBSD create that default 64k freebsd-boot partition. When you create partitions later, be sure that a) the start sector % 2048 == 0, and that b) the partition size (sectors) of new partitions % 2048 == 0. IOW, if you get the start sector correct and specify your partition sizes in megabytes, all should be OK. [It doesn't hurt to double-check your numbers before placing file systems and/or RAID on the partitions.] It won't get gptfdisk/gdisk into working automatically with 2048-sector alignment, but at least the alignments will be the same.