Yes, i've seen that as well, to a certain degree.
I've attached a map in which this is used (yesss, more ugly online maps - no, I did NOT make this one!!)
The map is 7 vs. 1; all vs. the player who controlls the visceroids that are in the middle.
In final sun you'll see that the viceroids are set to the gdi house.
Every time the "gold" player was on "gdi" side, that player would own the viceroids.
When the gold player was nod, red got the viscs.
Further than that though is only guesses.
I could bet though that if one player was gold & gdi then they'd start at waypoint #0 owning all of the "gdi house's" stuff,
and if the other player was nod & red that they'd start at waypoint #1 and own all of the "nod-house" stuff.
Just thought I'd post that, to whatever help it might be