Is there any logic behind why there would be a multiplication factor for rotarys, and not two stroke piston engines?
Nope.
It was a matter of protecting what was already established by restricting the new and unknown. Imagine you're on the SCTA board back when the rotary motor started to make its presence. Word on the street is this little motor makes hellacious power and spins to 11,000 rpm with only 60 cid. Man oh man that's going to put a world of hurt on the old pushrod/connecting rod guys. So what did they do? They looked at it, realized it had a three sided rotor, and said "Well this thing has a three sided rotor so it must some how pump out three times as much air so lets take the actual CID and times it by three". Brilliant!
Fast forward a whole bunch of years and they (you know who you are) realize that they made a boo-boo and attempted to fix it. The change went through all the appropriate channels and was okay'd TWICE before being rescinded. WTF? A little technicallity screws everything up. Somebody starts crying the blues because they're going to lose their record.
But it's okay. Pete (the OP) is going to handle the record in question. We wouldn't want anyone to get their feelings hurt because they lost their record to a RULES CHANGE (which has happened MANY times before). Oh no. Pete is building a new race car and a new race motor just so he can go out and take the record away from it's current holder. This way the record will be Pete's and when the rotary restriction rule change comes down the pipe again guess who will be losing his record? Pete will so no one will have any reason to cry about it.
Pete, I wouldn't worry too much about it man. They know they were wrong, they tried to fix it, but then they screwed it all up. Just follow through with your plan. It means parking the RX-7 but oh well. You'll go plenty fast in your new Ford Ranger.
Now if only we can clean up this "Tuner/Sport Compact" disaster. Talk about FUBAR...