I've set flags for certain hashes for releases with the same hash, but are significantly different, like different localizations. For these releases, when the tool encounters one of the flagged hashes, it looks for other files to differentiate which release it is, like checking the readme for the language. It would be a simple matter to have it look for the existence of a file that is unique to your patch.
As to ScummVM, there are a number of fan AGI games that fail in DOSBox with the original interpreter as well as non-PC releases that may only run in ScummVM or other modern interpreter or emulator. The app's toolbox already includes some. DOSBox ECE for DOS games, AGILE is the tool's default for AGI games, and WineVDM for Win16 games/installers. And I include AppleWin for the early Apple games. At some point I might incorporate ScummVM into the tool. I would not include it with the tool, but have it interface with the user's previously installed SVM.