I usually train at sea level but occasionally at a moderate altitude of 1100m (3500’). Threshold sessions at altitude do seem harder and heart rate is higher, but this could be because I don’t have a good fan there. Assuming altitude is a factor though, how can the session be adjusted or rated so that TRAI can account for it appropriately?
Altitude is a factor. The research says 3-5% less aerobic power available at those elevation changes.
TR AI does not currently account for altitude - it is something that has been suggested before though.
Just rate them appropriately, move on. You can try dropping the intensity 3% and see how you do when you’re at 1100m/3500’
I agree with @BCM.
Just do the prescribed workouts. You can adjust the intensity so that your RPE feels close to how it should, and then make sure to rate the workout based on how the work actually felt. We’ll make adjustments to your upcoming workouts based on your performance.
There isn’t really a good way to do this if you’re regularly moving back and forth between high and low altitudes, but if you’re spending longer periods of time after moving around, this should help. 
Thanks for the workaround to ensure the workout is completed successfully. The issue I was really concerned about though is that the capacity to produce watts for a duration is skewed downwards and affects future workouts and FTP prediction. Of course, over time this makes no difference at all so not actually a problem. Odd that at the same time I posted this question I notice others have raised the same. Certainly might be worth having an altitude adjustment dial available if this could be done without introducing other problems, maybe like altitude doping by the unscrupulous! Keep up the good work!