Have you tried just installing on the external disk without blessing and boot FreeBSD
Yes, I have tried that. While the Mac Mini Startup Manager alllows you to select the disk, it doesn't detect or start FreeBSD from it. I get the same error / output as I described above.
Problem is probably SIP now
I do not think so - SIP comes to picture only after macOS boots. This seems more like a firmware issue.
Given your use of macOS: I assume that you'll want at least a desktop environment, maybe much more, on FreeBSD.
True. I only plan to use lightweight WMs - either JWM or FluxBox that only need a few MB's of memory to run (I have already experimented with FreeBSD + Fluxbox on a Virtualbox VM with 2 GB RAM and it seems to work fine). (If I remember right, bigger swaps were necessary once only because RAM was limited and expensive. That is no longer the case and I think 1 or 2 GB is more than sufficient for today's modern system that have both faster processors and larger capacity RAM 8+ GB. I did read that ZFS does need a lot of RAM (though it frees it as necessary), and thus had a doubt if you suggested larger swap size keeping ZFS in mind?
Bigger pictures include future readers who might have the separate issue. Thanks.
Agreed - as per your suggestion, I have started a new thread here - FreeBSD 13 not Booting from External HDD on Mac Mini (Late 2012).