I don't understand what the problem is. If you are going to sail a boat in a mixed fleet then you'd be a bit silly not to take the best rating from the system being used for that particular regatta. The Viper in particular seems a pretty versatile piece of gear as it can rate with the heavier 104 group which seems to be popular in parts of Europe, then it can compete successfully against the lightweights when sailing in events governed by F16 formula rules. And it doesn't necessarily need to be steered by professional sailors to win F16 events. The most recent Australian National Title was won by a Viper with weekend sailors on board.
The various measurement rating systems seem to have taken a commonsense approach to formula classes by giving them one rating. Imagine trying to do individual ratings for all the A Class designs around the world!
Perhaps I misunderstand your comment on measurement certificates Wayne, but I'm very surprised to hear that you don't need a certificate to participate in an F16 start. Seems essential for a formula class to me. If you don't have a measurement certificate don't bother turning up for any regional, national or world event in A's that I've attended. That's also the case for F18's in AUS I think.
Anyway - gotta go and wash my sailing gear now - pretty cold sailing day here today - 21 degrees centigrade.