Since 2.2, you don't need anything special to compare ZIP, ECMerge contains a converter for ZIP files.
Here below are several converters settings you can use to expand ZIP, RAR, 7Z archives and compare them. You can define your own converters using third-party software.
C:\Program Files\Ellié Computing\Merge\converters\un7z-conv.bat (your location may be different)
Arguments
$(input) $(output)
The C:\Program Files\Ellié Computing\Merge\converters\gzip-conv.bat, unrar-conv.bat, un7z-conv.bat batches assume that you installed gzip, WinRAR and 7-Zip in C:\Program Files. If you wish to install them in another location, you can update these batches.