The flight test for the initial issue of an IR requires all items to be tested in the aircraft. The synthetic trainer test allowances only applies to renewals.
I could have said more about the oral section of flight tests: You will be questioned on any knowledge areas from the relevent theory exam that you got wrong in the exam. A 'Knowledge Deficiency Report' is sent to you as part of the exam result advice and you'll have to bring it to the flight test. You'll also be given scenarios pertaining to the level of licence/rating the flight test is for and asked to solve/apply the relevent rules to the situation. Knowledge about the test a/c limits etc can also be asked.