The way I'm looking at it (going for my current gym challenge as well) is that the battle will start in Gen 6 and so will go by Gen 6 rules. For those battles that had already been accepted (mine vs df, pwne vs emma, etc) the gym leaders accepted rule will be used. If mega clause was not specified, it will default to zero.
So basically all gym challenges from hereon out are gen 6 rules and require mega clause numbers to be specified.
Maxim's two challenges are the exception as he specifically requested to remain gen 5 rules until he revamps his gym for the two outstanding challenges.
Also,
Frosty if you know which ones are missing that would be nice, I updated IAR vs Lou and wasn't aware there were others outstanding