Yes good point. OK lets hit two birds with one stone.
To convert a color image file_C.png and an alpha mask file_A.png into an RGBA transparent file.png you can call :-
composite %1_A.png -compose copy-opacity %1_C.png -depth 8 %1.png
in a batch file using image magick and pass in the name 'file' as the batch file parameter ( %1 ). Then you can call that batch file from another with a list of files that need converting if you wanted to - which is similar to what I do for Kimmo's character tokens.
In my app you load them in as a pair - see image - and save out the corresponding file.