It’s important to remember for the discussion and questions that have been asked, Neptune is a 6-year old project started shortly after the release of Pluto, so a lot of the features Pluto currently has (like easy cell disabling) may not have been implemented when Neptune began.
So, rather than rehashing here (unless there are new questions), read the original Neptune announcement (Announcing Neptune.jl (now updated to multi-line cells!)) which has a good discussion on its intent and reasoning.