The vibe I generally get from Graphene users is that they feel that they are taking control over their device by installing Graphene onto it (which is almost always a manual process, at least for now). I probably exaggerated when I said the vast majority of users care deeply about this, but I think it's still a major selling point of Graphene for a lot of people.
And yes, I do agree that sandboxing actually provides more control to the user, not less! I'd just hate to see Graphene become more like iOS over time and start intentionally omitting features that would otherwise empower the user, for security's sake. If "security" and "giving users a say in how their phone works" really are diametrically opposed, and user freedom isn't a concern, then it would probably make sense to start gutting out stuff like developer mode, adb, and sideloading for the user's own safety. But the project's track record has been pretty good so far from what I can tell, and I don't think this will happen.