To reproduce:
1. Open an Attached Unity project "Rigidbodybug"
2. Open scene "scene"
3. Window --> Physics Debugger
4. Press Play

Expected result: Both manually written and code generated radius should result in the same size of the rigidbody
Actual result: code generated radius affects the height of the rigidbody

Reproduced on: 5.6.0f1, 5.6.0f3, 5.6.0p4, 2017.1.0b3
Can't test on 5.5 and older versions of Unity since Physics Debugger was not yet implemented.

Note: ''CapsuleRadiusByCode'' and ''CapsuleManuallySetRadius'' are exactly the same except that ''CapsuleManuallySetRadius'' radius is set to 0.25 in the editor
and ''CapsuleRadiusByCode'' radius is set to 0.5 but changes to 0.25 when in play mode.
Note: in attached picture playmode.png on the left is ''CapsuleManuallySetRadius'' and ''CapsuleRadiusByCode'' is on the right.