I'd wager they are more concerned with preserving their paid revenue stream than losing a few free users. Any company offering a freemium product has to strike that balance.
I don't seem to have a problem using separate installers for something like Blender, but the activation energy seems too high for installing "small" utilities[1].
That said, if I could get larger applications from Ninite, I'd pull from there in a heartbeat!
[1] Utilities may not /actually/ be small.