Thing is reps are wrong ALL THE TIME, and the Manual has tons of errors in it. I am inclined to believe Marcus from mesa because hes one of only like 3 or 4 CS reps at mesa. He works with R.S. himself, if he needs to know something, all he has to do is ask the guy. Heck Marcus is the one doing the demo's in the demo videos!
Also consider that even though your amp works, it may not be biased correctly now. Its my understanding that its not really dangerous to run the el-34 in 6l6 mode, but it is dangerous the other way around. Also consider, if it didnt matter which tube type you used then there would be no tube switch. Either way the switch is set, the sockets are set up the exact same way, either for 6l6 or el-34. if it was an either or thing, then there would be no switch.
From expeirience in biasing my bugera, i noticed with 6l6's in , if i switched the bias switch to el-34 the bias jumped up dramtically ( as in got way hotter). So an el-34 and 6l6 configuration is definitely not interchangeable.
It may function the way you have it, but i guarantee the bias is not optimal.
But in the end, if you like the sound, and the amp doesnt blow up, then... its the right setting for you.
~mike~