I do not use formations generally but I believe the OP is trying to produce the same formation regardless of driving toon. Typically we move our box by focusing on one screen and have the other 4 on auto follow. When the team comes to rest the group looks like this in top-down view mode

--X--
-----
--P--
-----

Where X is your driving toon and P is a pack of toons often overlapping each other. Now assuming P is 4 toons label A, B, C, D and each has their F key mapped to a different movement directions hitting 'F' will produce the following pattern.

--X--
--A--
-B-C-
--D--

However in FTL you can drive with any of the 5 toons. So if you are driving with toon 'B' and you enter a formation your groups ends up like this.

-B---
--A--
--XC-
--D--

Also if you rely on the formation key to break auto-follow you have the problem that X is still in auto-follow mode to B.

I believe the OP is looking for a way for X to inherit the movement key of B in the formation key while B is leader so hitting the formation key has the exact same result regardless of the driving toon.