Although I haven't done the combination of BIOS and GPT, I have done BIOS and MBR. For what it's worth, I've always had some difficulty booting FreeBSD from a Debian based system (chiefly Ubuntu and Mint), and more success booting from a RedHat based system, (CentOS and Fedora.) VoidLinux and ArchLinux have also worked well for me. I don't know if it's worth your trouble to try one of those distributions (or your use case, whether it's even practical to do so), but I can have the same 40_custom on Void and on Mint, and it works on Void but not on Mint. I've never really investigated thoroughly, and these days, do everything on UEFI, (where Debian based distributions still don't work).