I flew my 3" Hawk Mountain Talon "Back in Black" many times with no tracker. One weekend I installed a BRB GPS into the AVbay on the opposite side of the sled from the Raven altimeter. It flew once in this configuration to 9300 ft on a LOKI L-1300 (video
here). The next day it flew again in the same configuration - except this time, despite the raven indicating 4V and 4 good charge continuities on the pad, absolutely no deployments occurred. It came screaming back down at us and buried itself into the ground. All the electronics (a Raven, a BRB GPS, a BRB beacon and a Contour camera) were utterly destroyed - so I have no way to verify what happened. But given that I am a veteran of flying the Raven many, many times I am fairly certain there was nothing amiss with it, the power perch or the battery. The altimeter, perch and battery were secure with no chance of disconnection during flight. Given the battery voltage and continuity beeps on the pad, I am left to assume that the transmitter in the avbay somehow interfered with the raven. The BRB GPS transmits every 5 seconds or so for a brief burst. I think I got lucky the first flight, but on the second the transmitter burst came at just the right time to freak out or confuse the raven.
So, even if you let the combination sit and cook - and you don't see any unintentional deployments - remember that it is also possible for the transmitter to interfere with the altimeter such that nothing deploys when it is supposed to. Believe me, this is terrifying - especially if you've never experienced such a failure before. I was sure that someone was going to be hurt by my rocket. That would have destroyed me.
Could you mount that tracker such that the antenna is outside the end plate of the avbay? The end plate may be too thick to allow the rp-sma connector to protrude far enough to install the antenna. If it is possible, so long as there is sufficient airframe attached to that end of the avbay after deployment, the antenna should not be beaten up by the recovery hardware. The ejection charges will foul the antenna, but it can be replaced if this ever becomes too big a problem. The aluminum end plate would block the vast majority of the radiation from the antenna being injected into the altimeter. There will still be some radiation in the bay from the tracker.
A better solution would be to put the tracker in the nosecone. Then it's far away from the altimeter. If you use an aluminum bulkplate or aluminum foil on the inner surface of the nosecone bulkplate, the chance of interfering with the altimeter should be all but eliminated.
I will never fly a tracker in close proximity (on the reverse side of the sled) to my altimeter again.