Yes, one can mute boosts only, but the 400-count still includes all muted boosts, even if I don't see them.The posts that have been pushed out of my TL by those boosts are gone. I can find them only by actively visiting the profiles of the people I follow, eg through lists.
It's a design flaw. We can live with it, but we have to be aware of it.
Hence I am cautious with my own boosts, conscious that each of my boosts pushes out another post in each of my followers' timelines.