While CIC did not divulge the details of workflow, I found three links down below the Application Status page on ecas which gives fairly an idea of how my application will flow. The workflow is more internal and would define who my application will pass through and relevant conditions. our question is around a particular condition to decision making. I have seen pregnant spouses landing on PR, but not one with a deferral letter. Hopefully someone in same scenario will respond.
You might consider submitting this question in the family class sponsorship section?
they haven't really released the stages of applications so anything people know is at this point guesswork. However, your application will be on hold until your wife's completed a full medical after the baby's born.
That's right - you should expect nothing will happen until your wife gets her xray done. CIC will effectively put your application processing on hold while they wait for the xray to be completed.