That's because, as Ramin (ex-YSAC president) put
it when Yale A had to play Yale APTP(*) in the first
round of the playoffs at Penn Bowl 9, "at least this
way, one Yale team is guaranteed to advance to the
next round."
Anytime you have a situation where
teams from the same school are split across brackets,
you need to exercise care in setting up the brackets.
IMO, pre-establishing the brackets in such a situation
is inherently unfair because it means that certain
teams are at risk of being forced to play one another,
while other teams are not. Seeding teams numerically,
or doing a random draw for bracket pairings, is far
preferable.
--STI
(*) Yale A Past Their Prime (i.e., the Yale A team
from 1998-99).