Then I was thinking of another distribution, probably. There's one Berkley software distribution that doesn't come with any window manager or any thing, just meant to be ran as a headless server. Won't be surprising if it lacks some libraries and tools needed to compile something like godot. But I guess that's not it here then.
You might want to take this to the tracker then. Pretty sure godot should be straight up compilable on BSD so if it's not working then there is a fair issue to report, just make sure to search the tracker first to see if someone has already reported the issue.