Ok so as I understand it the secondary throttle opens later than the primary so in theory secondary bridgeport should remain closed as well (I'm not talking about port timing but throttle butterflies).

So why does it pull low idle vacuum and need to idle higher and also has the brap brap idle? Also why does it affect low end? Do most builders eliminate the secondary throttle?

 

This was covered many times. Overlap is always there, no matter if runner is opened/closed. Low end is vague term, every high overlap engine will suffer from low load operation at any RPMs, but give it enough load, and it has more power everywhere-of course, free flowing intake and exhaust is mandatory to take advantage of ability to breathe. To answer your questions, low vacuum is caused by exhaust dilution-rather then trying breathe through closed throttle, engine is pulling large amount of exhaust gas. Brap brap is caused by triple misfiring-nicely described in "Rotary engine by Kenichi Yamamoto".