Then why do most dealers offer the SERT and every other type of performance muffler and intake accessory if the bikes are supposed to remain unaltered?
Same reason the MoCo sells all that "Race Use Only" stuff to the dealers, to relieve you of more $$$$. The fact that the EPA turns a blind eye to all of this doesn't mean what Harley and it's dealers do is even remotely legal, it isn't.
I would assume you will need to direct your question to the folks who make motorcycle dynomometers. There may be some out there that were designed to handle trikes, but I'm not personally aware of one. Fortunately, with some of the features available on the latest TTS or SEPST you can do a reasonable tune without a dyno. Ask the experts on the site about doing a V-Tune or the SEPST equivalent.
As much as I love to rag on H-D, I have to agree with RedDevil. It's not Harley's fault that chassis dyno's for three wheeled motorcycles aren't available. If you want to blame H-D for anything, blame them for putting out a product that is so poor in stock form that it needs modification and tuning to run worth a chit.
Jerry