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I seem to get different results from the following two command lines. I do not understand why the second shows any transparency (faint checkerboard pattern). Perhaps I misunderstand what it should produce. But I expected the two results to be the same. Is this a bug or have I made some error in the command line or my understanding of what to expect?
When we compose one pixel over another, if either is opaque then the result will be opaque. But if they are both (partially) transparent, the result will also be (partially) transparent.
Your first example doesn't have alpha enabled, so "-channel a -evaluate set 50%% +channel" does nothing. If you prefix that with "-alpha set", the result is partially transparent, as expected, and "compare" says the two results are the same.
"-compose copy_opacity -composite" doesn't need alpha to be enabled. Indeed, we often deliberately turn it off, as you have done.