This is due to MAE's default way of storing files in AppleSingle format. Mac OS files have both a resource and data fork, and MAE must handle these files differently on a UNIX File system. To accomplish this, AppleSingle is used where the resource fork information is pre-appended to the data fork and creates one file. This combining of files creates the larger file you see in UNIX.
You can change this default, from AppleSingle to AppleDouble, by launching MAE with the "-filedouble" option. This keeps Mac OS files as separate data and resource forks. From within MAE, AppleDouble files will appear as one file, however within UNIX, you will see a file name "name" (the data fork) and "%name" (the resource fork). Then the file "name" will then report the same size in UNIX as in the Finder.
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