The german and french versions on GOG are normal installations of Archimedean Dynasty. In the english version there are some changes to the installation. These changes don't affect the gameplay:
- all files from the CD image were copied to the Dosbox harddisk. For example the GFX\MVI folder. This causes the english version to be bigger. (fun fact: if you remove the "imgmount" command from dosbox_ad_single.conf, the english version still runs without music during the missions, in the german and french versions the game doesn't start anymore)
- the music during missions is played from the MUSIC folder instead of from the CD image, and the music tracks were removed from the CD image. (I find it unfortunate that the english version doesn't include a complete CD image.)

No idea why the english version is different. My guess:
GOG worked on the english version first. I remember that it took some time to get the game running well with Dosbox, so they probably had to tinker with it a lot. When the english version ran, they didn't clean up this tinkering. For the german and french version they did a clean install.