It does.
The NCS “base” divisions are not like those in other sections. They just matter in two ways:
1. The section has always had a 0.500 rule where you had to finish at least that overall, in league, or… against teams within your “base” (i.e., enrollment) division. The base division includes non-NCS teams that have enrollments within those divisions (all like-sized schools they played).
2. If a team does not qualify for D-Open/D-1, then a base division may limit how much higher or lower they can compete in the playoffs. For example, Cardinal Newman has a base division of 6. If they are not among the top 8 teams in the section, they can still make the playoffs, but in no higher than D-4. Deer Valley, being a member of base division 2, cannot play lower than D-4.
All teams are eligible for D-Open/D-1. The top 8 teams are placed there, then the next 8 are in D-2 (with the above stipulation). The divisions and seeds are supposed to be determined by the Maxpreps (really, Calpreps) ratings.
That said, there can still be a human element “for the good of the bracket”.