Let me preface this by saying that I never studied fluid dynamics. I'm not a mechanical engineer, and this is all speculation.
If the EBC is referenced to absolute manifold pressure, as would be the case with a MegaSquirt for instance, then the power loss will be much less than what new2mud proposes. Closer to zero, in fact. Because the pressure ratio of a turbo is variable.
If you have your EBC set to make, say, 190kPa of manifold pressure, then it will hold that pressure whether you are in Death Valley or at the top of Mt. Washington. Obviously there will be some power decrease as the efficiency of the system will go down slightly (the turbo is having to work harder, and making more heat) but it will not be significant by way of comparison.
Now that I think about it, a ball-and-spring MBC should, in theory, be the same. They operate by pitting MAP against the tension of a small spring. Ambient atmospheric pressure should have no effect on this.
Given the above configuration, what you should see, ironically, is more "boost" as your elevation increases. That is to say that the ratio of the pressure in the manifold to the pressure outside will increase, not because MAP went up, but because atmo went down. Remember that boost gauges (particularly those marked in inches and pounds) generally read pressure relative to the surrounding air.
Let's say that you have your boost controller set to hold the aforementioned 190 kPa. At sea level, baro is about 100 kPa, that works out to 90 kPa above atmo, or about 13 PSI of boost. Your boost gauge will read 13 PSI.
In Devner, the ambient atmosphere is at about 83 kPa. Your boost controller is still going to make 190 kPa in the manifold, and this is now 107 kPa above atmo, or about 15.5 PSI of boost. Engine power will remain the same, because MAP remains the same. Boost, as we generally think of it, is relative.
This works because boost controllers are essentially a closed-loop system. They adjust their behavior to achieve a pre-set manifold pressure, and they shouldn't give much of a damn what's going on around them. A turbo which is operating on stock can pressure might be more affected, as the plate inside the can has atmo acting upon one side of it, but I don't think this is going to be signifigant.
Now, a supercharger is a different story. Unlike a turbo which is able to adapt its compressor speed to suit the occasion (by varying the wastegate opening) the supercharger operates at a fixed pressure ratio determined by its pulleys and lobe design.
A naturally aspirated car driven from San Diego to Denver will lose 17% of its manifold pressure by the end of the trip, and be down 17% on power. That much is easy.
Say that a supercharged car is designed with a pressure ratio of 1.5. At sea level, that's 150 kPa MAP, or about 7.35 PSI of "boost".
In Denver, atmo is 83 kPa, so the 1.5 PR
makes for 124.5 kPa of MAP, 41.5 kPa above atmo, or about 6.1 PSI of "boost". And just as before, we're down 17% on total air mass.