I noticed in the logs that the red/blue teams are combat log split during the phase, so you cannot see the DPS from your raiders on the other team. This leads to inaccurate numbers that are going to randomly skew data on WCL. But whatever, turn off allstar points there.
Something interesting that may matter... some forms of AOE/cleave go through the two team phases. Stomp for BM hunter pets, as well as sunfire/solar wrath/lunar strike for boomkins. It seems that it essentially cleaves on itself -- you hit your phased version, but the cleave also hits the one in the other phase. This means a few things:
1. Cleaving the boss will get out of phase faster -- might matter on mythic.
2. In theory you could have 4 BM hunters and have each send their pet at one of the clones and auto-detect which is the right one.
Solving it is easy with raid markers, sure, but automatic solve is good too.
Anyways, I don't really have anywhere to go with this information, so figured some might find it useful or interesting.
Edit: looks like almost all AOE goes through if ground based. Like tank DH sigils, for example. And thrash for feral druids, which you wouldn't think is ground based but maybe?