Are they though, structurally? The dead three themselves are just distant entities, not characters we really deal with, beyond having brief exchanges with. We don't get a chance to feel anything towards them as antagonists. The netherbrain isn't really the central antagonist until the very end. Before that it's not a character, it's just a force of nature at best, but it takes focus from the chosen, who should technically be the central antagonists by virtue of being the most active antagonists. But we don't even know who they are until the end of act 2, at which point their big concern is the netherbrain that isn't even a character.
There's no focus, same as every other part of the main plot.
Lots of media have more distant/mysterious antagonists, so for me, it's not the biggest issue, it's that it's not well executed. Even if they are not as present, there should be some incentive for them to feel like antagonists.
