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MFI is a reference system that has no idea how much air flow there is at any time.
I am rusty on MFI but things like the altitude can and the thermostat act on the position of the injection pump rack which determines how much fuel is metered at any time. Messing with shims is like shortening the linkage rod to the pump. It is a short cut for just adjusting the pump correctly. Over time a pump can go out of spec and external adjustments may no longer be sufficient.
Add to that possible air leaks about the throttle plate shafts and there comes a time when the TB's need to be rebuilt and the pump calibrated on a bench.
From my limited info, messing with the height of the altitude can makes no sense. One might get lucky and stumble on something close to the correct air fuel ratios but it is not the right way to do it and you will loose the intended correction the altitude can provides.
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