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appimages are compressed so there is some overhead in accessing the files, this is expected. How much this impacts performance depends on your hardware but I don't think it's a big difference in most cases, I would advise to document this in the wiki and it leave it at that.
Apparently AppImages run faster when they are first extracted:
./FreeCAD.AppImage --appimage-extract
See thread on reddit which contains a batch script to automate this: https://www.reddit.com/r/FreeCAD/comments/1fv69g2/breaking_out_the_appimage_for_faster_response/lqc8l5r/
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