Has the M&M III copyprotection been bypassed in GOG's version? Everytime I start up the game, it speeds past the copyprotection screen without requiring me to input any key word from the manual. I tried slowing the game down through DOSbox and the same thing occurs.

That's what it should do. It bypasses the question so that's why it skips it like that. Otherwise you wouldn't be playing the game afterwards ;)

What puzzled me is that there's a PDF file with all the key words in the M&M III folder.

It's almost certainly part of the Limited Edition version that they got sent from UbiSoft since that would not have the DRM checks removed, but instead would have such a pdf file.

That PDF is useful... since it has the World of Xeen keywords, also... and unfortunately it doesn't skip it on that game.... Well, unfortunate for those who don't also have the CD version. :)