We use the tourney lists as our basis. We do allow variants from SFOS adjusting what we think is necessary to match as close as possible to the original tourney ship. In addition, we allow the extra rules for each fleet, ie emine variants, EA missile variants and so forth. Things seem pretty balanced for the most part.
Edit: I think this thread may be more useful if people point out what fleets they use and what fleets they fight. I think a big part of thinking the SFOS or tourney rules is balanced on who your opponent is and who you are playing. I would suspect we would see a lot of similar data. For example many people who see Centaur/Narn battles may say the game is balanced. Those who play Narn/Shadow battles might say otherwise. This might, at least, give the playtesters more data to go on as to which fleets need adjustment.
For me it has been ISA/Narn. In SFOS it wasn't even close. In the tourney battle, it seemed about right. Bad rolls on either side and you would lose. And trust me, I have tried a LOT of combinations to defeat the WS. It just didn't/wouldn't happen until we tried the tourney WS. Having said that I could see the WS maybe getting 5AD with the secondary weapon.