Hello jrp,
The coordinate information from two points only is not sufficient to set up the coordinate system due to the rotational degree of freedom around the vector connecting two points.
So for the coordinate system definition you'll need three points, even, if the positions of two of them are known relatively to the third point.
To use special cases for these purposes I can suggest to use custom Python scripts, as implementation of multiple different options in GUI doesn't seem reasonable, as each case may be necessary only for one user.
So if you have some custom requests, you can post a topic in Python scripting section or send an e-mail to support@agisoft.com with the description of the case and desired functionality and we'll assist you with the custom scripts.