The ordering is based on how most guilds go about the progression. I also look at total kill amounts for serverwide progression. In this case, it's kind of a toss up. Most guilds do Kael before CC, however CC does have a couple more kills than Kael gamewide. If that number increases, I will probably flip them around. But for our little server, the standard so far is SL > Kael > CC.
Mid tier flagging has never effected how RBK breaks up raid progression by tiers. Raids that require flagging are naturally at the top of the list (the final raids of the tiers to be completed).
RoF has been a mess so far for our server lol. Guilds are all over the place, it makes tracking a little weird for sure. I'm always open to suggestions, but please don't take offense if I don't implement them.