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For instance, my 5D tends to overexpose by about 1 stop with my Rokkor 58/1.2 when wide open, so I consistently have my EC set to -1 when using the lens wide open. Throw .73 stops more error into the equation and I would then be consistently stuck at -1.66 EC, which gives me very little room on the low end of the EC scale to compensate for other exposure factors.
I think the fully silvered mirror would tend to make the camera underexpose due to more light going to the metering system. Therefore, if you normally set EC to -1 you would only need to underexpose by one-third of a stop with the new mirror, still giving you almost the whole range of EC still available. However, I do agree that correcting for the fully silvered mirror using the custom function as you suggested would be the best way to handle it.