Most gamer input hardware such as mice and keyboards (not cheapwad bargain-bin grandma kind of hardware, but products from companies like Logitech for example) come with programmable software that let you customize your device on a per game/application basis. The software can run at OS startup time and put itself in the systray then monitor for when you launch a particular game and activate a custom profile for that specific game for you automatically. It does this by monitoring for the game's specific executable to be loaded, and while you can customize the location of the specific .exe file that is used to activate a particular profile to match a specific game, if you have multiple profiles all pointing to the same executable, the software can't tell which one of the profiles to load that you may have configured.

If all DOSbox games used one single DOSbox installation, then no matter which game you load inside that DOSbox, to the operating system the only piece of software running is DOSbox, and that is what the Logitech profiler will see - that you're running DOSbox, so you can only have one profile for it which ends up being used with all games.

If one has such hardware like this (virtually any hardware made by Logitech) and uses this optional software (Logitech Gaming Software), you must have a separate executable for each game in order for it to detect that you are running a specific game and load the correct programmable configuration customizations for that specific game. The only way for this to work is for every game to have its own unique executable to launch as Logitech software can't look inside DOSbox as to what's running in it to determine that (not in any easy way anyway).

Of course this problem doesn't affect people who do not use such software or care about it, but there are enough people out there that do that it is a problem worth not having to deal with. Surely the number of people who worry about multiple copies of DOSbox on their hard disks is much smaller than the number of people who want to be able to use custom input hardware profiles with all of their games regardless of whether they are a DOSbox game or not. :)

Aside from that though, GOG tests games with specific versions of DOSbox, and newer versions of the software may cause a given game to break, or cause other random quality control issues. It would be an extreme nightmare for them to try to use one single version of DOSbox across the entire catalogue and either never be able to change it for one single game, or to have to update every game regularly for every version of DOSbox that comes out. The only sustainable solution that is sanely supportable by GOG is to ship each game as it's own ready to use supportable all-in-one package.

It's perfectly fine for people to experiment with running GOGs games in their own custom DOSbox installs of course, but there are extremely good reasons that every GOG game ships with and installs its own private copy of DOSbox, and for all intents and purposes it should be considered a part of those games.

I suppose it is also worth noting that if someone is worried about duplicate files of multiple games filling their system, consider that there are tonnes of games that install their own private duplicate copies of DirectX 8, DirectX 9, Microsoft VC++ runtime libraries, the bink video DLLs and literally hundreds if not thousands of other duplicated DLLs and other files. There's just no sensible way imaginable for GOG to try to avoid that kind of duplication and still have supportable products, and it's also next to impossible for the end user to try to undo this duplication themselves without breaking how GOG updates work by changing each game's folders in a highly customized manner. In short it just makes the customer a lot more work for themselves over the long haul that isn't really worth the time and effort IMHO.

Besides, if someone wanted to be smart about removing disk wastage due to file level duplication, there are a few things one can do much easier than all of this. The first is to use 3rd party software to search for file duplicates on the given hard disk and replace them all with hardlinks so there is just a single copy of all of the duplicate files existing in actual allocated drive space, but multiple filesystem references all pointing to this single copy of the file.

Even though Windows does not itself provide an easy end-user way to create/remove/manipulate hardlinks (like an OS like Linux does for example), it does support them in the underlying operating system and 3rd party tools are available that can be used to make this functionality available in the GUI. I use a Windows Explorer addon called "Link Shell Extension" for example which adds the ability to create/remove/manipulate hardlinks, symlinks, junction points and a number of other admin type features to Windows Explorer. That software itself would not be a good solution to this problem however as one would have to manually scan every game directory on their own to try to find duplicates and replace them with hardlinks.

In Linux there is a program called "hardlink" written by Jakub Jelinek which does exactly what I suggest above, it can scan a hierarchy of files on a single filesystem to find absolute duplicates and optionally replace all the duplicates with hardlinks to reduce disk space wastage. Doing this removes all of the wastage but without altering the way any of the software itself works. So for example, despite the fact GOG installs separate copies of DOSbox with all the games, any identical copies of DOSbox would all be replaced by one single copy of that version by using a program like "hardlink" under Windows (I have no idea if it is available for Windows though but it is possible it might be available as part of Cygwin).

Another way to free up disk space is to selectively use Windows' built in disk compression on a per-file or per-directory basis.

The combination of these two techniques would free up tonnes more space than obsessively worrying about multiple copies of something like DOSbox ever could dream of freeing up, and with a small fraction of the administrative overhead. The only key to making it short and quick is someone interested in trying to do this to do some googling around to see if they can either find the program 'hardlink' for Windows, or some other Windows specific software that has similar functionality. I know there are tonnes of programs out there that can search your hard disks for duplicate files and delete dupes, and it just may be possible that one of them can optionally use hardlinks instead so that the duplicate filenames remain in place everywhere for applications to continue to function properly and upgrades to work right - but without making a huge mess.

Alas, I'm just the idea man planting idea seeds ... someone else has to seek out such tools themselves, but I'm sure they'll be rewarded if they decide to speak to the Google. :)