I believe these vehicles would still allow takeover without the key in the port since it's the same setup as the models with keyport and the push-to-start button. The car is already running and does not need to see the key anymore. Inserting the key in the key port is required though if you want to be able to shut the car down later on.
Takeover itself will not work if the module does not see unlock from the remote. Meaning, if somoene breaks in, the starter will shut down once the door opens.
The key is not supposed to get locked in. Verify that the extra connector labeled "for 2009-2010" is not connected. It's part of the Key Release circuit (see installation guide without T-harness for reference) https://cdn02.fortin.ca/download/72791/evo-all_ig_sal_bi_aud-a4-a5-q5-s4-s5_2009-2014_pts_a_72791.pdf