hedwards: In retrospect I realize that you were probably referring to the DOS versions being used whenever possible rather than the Windows version.
GOG offers Windows versions of Earth 2140 (which has no AI) and Windows version of Incredible Machine 2 (aka TIM 3, which can't play CD music and has ugly interface). GOG also offers non-upgraded Realms of the Haunting (which has no control mapping), and Earthworm Jim 1+2 (which is not the Special Edition 1+2, but just two games bundled together). GOG also offers compilation versions of M&M 4 and 5 (which have no CD audio unlike the original releases).
So, GOG getting non-Gold Thief is still a possibility.