How do Ecoboost PCM's handle altitude?

I have a 2014 F150 Ecoboost and am curious how the PCM adjusts boost and airflow based on altitude(ambient pressure). I have spent a bit of time in the tune and have found nothing that appears to be any kind of adjustment.

Do they simply use the overspeed table(45559) under Engine->Airflow->Turbocharger?

The reason I ask is because I live at 6500' and I have multiple tunes from different tuners that seem to respond in different ways. My stock tune only seems to like to flow ~30-32 lbs/min at this elevation while most of my tow/performance tunes will hit in the 36-37 lbs/min range at around 50% WGDC. Then I have this one tune that tries to blow up my turbos. It will hit 38-39 lbs/min @ ~4500rpm and then it sends the WGDC to 100% as the RPM's keep rising. Luckily the wastegates must be blowing open and it appears that my turbos don't exceed the 220,000 rpm threshhold.

Anyways, just curious why some tunes would be ok and others not. What parameter would they change to result in the PCM trying to go beyond the maximum flow of the turbo at this altitude?

I don't have HPTuner software so I don't have specifics, but if you can search tables, look for Limiter Tables.
I have: Limiter Tables->Airflow Limits->Max, Turbo, WG Failure, etc.
There's one called Airflow Limit Turbo Baro. Comp. Pretty sure that's the one you want, and I'm pretty sure it's an OEM table so you'll likely have it.
All I can find on shaft speed is that it's inferred based on a coefficients table. Couldn't find a specific limit for that.

Have you tried using the compare feature to see what's different from one vendor's tune to another? This should narrow down which parameters it could be.

You would want to be looking at LPSI and other Pressure Ratio based calculation limiters. Usually as you increase altitude (and end up with a lower ambient Barometric pressure) you will see a lower allowed boost pressure limit due to the multiplication of Pressure Ratio times Ambient Barometric Pressure.

So where I am located the ambient BAR is about 13.9psi. I typically run a Pressure Limit of 2.70 which would be [2.70-1.0(one ambient atmosphere)]*13.9=23.63psi maximum manifold pressure. This isn't directly limiting it based on lb/min airflow, but they are related as a function of airflow being related to airload at rpm, etc.

You could also be seeing it trying to hit a certain PSI through another table, and with you being at higher altitude it would need to hit a higher pressure ratio to hit a higher Manifold Pressure. That may cause you to see a higher estimated Airmass/Airflow.