After reviewing the page I sent you to I realized it didn't cover much of how the altimeter bay was put together. With the timer in the fin can I was able to leave the airframe unobstructed. I alsways use motor ejection for a back up of my altimeter. I can't remember if the Intrepid comes with an altimeter bay set up because I usually scratch build one into every rocket. Look at my Der Big Red Max and my Horizon page on how I set up altimeters.
To answer your question...Yes, you can use motor ejection in the Intrepid.
P.S. I added some more flight pictures to the Intrepid page