Absolutely - the vast majority of the Adapt work we do here at Kineo is directly in the framework and tracked via version control - Subversion in our case since we find it's a lot easier for non-technical folks to deal with. We also find it's a lot easier when working with very media-rich projects - some of our projects can get into the region of 10 or 20GB (as high as 90GB in one case) with all the source files (PSDs and video) which is easier to deal with in Subversion as you can do 'sparse checkouts' to only get the bits of the project you need to work on - and don't need to keep the entire history of changes on your computer like you do with Git.
We also customise Adapt pretty heavily and it's a lot easier to do that when you're working directly with the framework.
Finally, we frequently build multiple courses from the same source - and as the Adapt Grunt task runner doesn't handle this we created our own task runner - RUB - to do so, it's well worth checking out if you're thinking about going down this route.
Let me know if you've got any other questions about this way of working and will do my best to answer them!