I talked to a dealer near me and he said it is common to have to drill a small hole through baffle sometimes, for the sniffer. He said he doesn't recall having to do it to Supertrapps though but it's no big deal if need be. He says it wouldn't make a difference in the sound, also.
Like I mentioned above, I'm going to see how it runs first, doubt I'll need it dynoed.

 

A good tuner has a spare closed end cap already drilled and uses this instead of yours, since so many people like the SuperTrapp systems. A closed end cap is not expensive. I use an open end cap on my S'trapps so it's not necessary, it's already "drilled" since it's open. Since you've already bought the SERT, I'd find a new tuner who knows what they're talking about. It's my position that this service tech is a "dummy", but what do I know, I avoid HD dealers like the plague and instead used HD-trained independents.