A few points.
There is a description of an early version of the scheduling software on the
Idle Loop website. The FMS may use a more recent version but let's assume the algorithm is the same.
The scheduling algorithm is stochastic, i.e. it has a random element to it, which is a standard approach for solving a complex optimization problem.
The particular criterion discussed above is "Pairing Uniformity" and it is one of the goals being optimized, but that has to be balanced against several other criteria including computation time.
Since the algorithm is stochastic, the "good schedule" metric isn't really
do the same teams play with/against each other more than once but rather
does this happen much more frequently than we expect.
Smaller events such as Western Canada or Toronto East have few enough teams that it's a mathematical necessity that the same teams face each other more than once.
Finally, most Regionals have 1-5 teams who play an additional surrogate match. If the purpose of this analysis is to see how it affects ranking then a team's surrogate match should really be excluded, although they would still count as a partner or alliance for other teams. (This is a small effect)