Autorun (which is often a problem with older Sierra games and has nothing to do with how well the game will install or run) and installation have nothing to say about the issues that are often encountered from the games during game play. There are several SCI Windows games that will install and run just fine, but have impassable bugs later in the game. most people aren't very happy when they play most of the way through a game only to find that they have to start all over again, because they have to switch versions and find that their save games don't work.
The SCI speed bugs affect both DOS and Windows versions, but DOSBox makes these moot with the DOS versions. The Windows versions often have odd bugs under XP, like the endless loop of "audio out" error messages that pop up in the Windows version of QfG4.
There has to be compelling reason to use the Windows version over the DOS version when there is a choice of both. The Windows version of KQ6 is about the only SCI DOS/Windows game that I want to run the Windows version, because of the much higher rez dialog images. Greater color depth might be desirable, but it is no where near the huge difference between the two versions of KQ6.