Make usage of Configuration.EMPTY safe

With current approach there is a high chance of making a programming
error and altering the state of singleton Configuration.EMPTY object,
because previously configuration was usually set by link to it.

This CL changes the behavior to create Configuration member objects
only once and alter their state afterwards.

Test: Manual and existing tests still pass.
Change-Id: Ie267c2fbf555f137670b7bd2cd251b817c69bc8e