I don't think it's a simple thing to just turn off spritesheets. Spritesheets are always power-of-two sized, and while WebGL 2+ supports non-power-of-two texture sizes, WebGL 1 does not. There's still enough WebGL 1 systems out there that I think if it just exported a bunch of non-power-of-two individal images then your game will be broken on a small percentage of systems, but enough that you'll get a lot of "game doesn't work" reports.
Then there's other issues like larger games losing the benefits of spritesheets could become significantly larger to download and significantly slower to load, and have a runtime performance hit too. It could be a massive deoptimisation for your game that slows things down even for players who don't want to mod anything and just play the stock game, which I think is an unfortunate trade-off.
Perhaps some of that can be mitigated in various ways, but it's complicated. Modding is a very large area if you want to go further to adding new kinds of objects, changing game logic, adding new kinds of level themes, etc. as well. I fear this may be one of these areas people say "just add A!" then "just add B!" then "just add C!" and then on for another 20 things over months/years.
Fair enough! I'll admit it's already possible for me to offer a set of in-game tools to the player to inject their own custom art and music and have those changes propagate through the game. I consider it a big hassle, but i guess turning off spritesheeting is equally or moreso a big hassle for Scirra.
Oh btw, to address your concerns with larger projects being slowed down by disabling spritesheeting; my suggestion was to have a bool in the export options to enable or disable based on the preferences of the developer. With enabled being the default option of course :)