If the ambient pressure is being measured, then the rate at which is changes in a particular medium is irrelevant and there would be no problems. Pressure is just a direct input to the calculation.
Maybe I'm missing something here. Like the point of watching GF99 as you drive up the mountain.
1. Surfacing M-value at sea level is calculated with the assumption you're getting (in and) out of the water at sea level. Surfacing M-value at 600 m is calculated based on the assumption you're getting out of the water in a mountain lake in Switzerland at 600 m altitude. M-value line is a straight line
because the pressure changes linearly.
In the air M-value line is no longer straight, but your dive computer has no idea. If you're getting out of the water at sea level and driving up to 600 m, the surfacing M-value at 600 m calculated by the computer is wrong for you.
2. Similarly, computer calculates off-gassing between sea level and 600 m up based on the assumption that ambient pressure drop is linear. If you're driving up in air, it isn't, but the computer does not know this. Your computed gas loading is going to be off.
3. GF99, as I understand it, is the ratio of calculated gas loading, as per #2, to the surfacing M-value as per #1.
To me this sounds like two wrongs. They may largely cancel each other out and make an almost-right, but personally I'd take Scubapro's little yellow mountains over GF99 any day.