This is where traditional tools shine. The reason braces are flush to one side is for the ease of joinery.

Sometime.... The best face/reference face is true and sometime is isn't. If the timber is diamond shaped you need to either call the reference face true or take into account it is out of square by X amount. Then there is twist/wind to take into account, if present.

There are situations where you can measure off either side from the best face of the reference face and be good. There are times when the Al B. square will not function as we wish. In these cases I use a framing square applied perpendicular to the reference face, taking into account out of square issues. I need to do a video showing this.