Answering my own question here 
. If I had just spent 10 more minutes I would have come across the answer.
Answer: You can pass build options from your build.zig to a dependency via the args parameter. Make sure they actually match.
build.zig
const lib_godot = b.dependency("godot", .{
.godot_path = godot_path,
});
Dependency build.zig
const godot_path = b.option([]const u8, "godot_path", "Path to Godot binary [default: `godot`]") orelse "godot";