Since you are not adding any conditioned square footage beyond what was already there with your existing system, why are they leading you into a completely new system? Is it just to get the integrated zoning capability? And $6,821 to retrofit three duct lines to the theater (two supply and one return I would assume), a new thermostat and a zone controller is downright larceny!!
You have more than enough "construction smarts" and skill to pull this retrofit off on your own. All you need is a bit of hand-holding and some good advice. When I was looking at doing the exact same thing that you are trying to do (converting single zone unit to dual zone), I ran into the same exorbitant charges you did - only my system conversion didn't include the air cleaner and was about $4500.
Not wanting to spend $4500 (or $6821 for that matter), I found this HVAC company
online that can take your input data of system size, duct sizes, air exchanges, thermal heat load of a theater (extra people, air tight, extra insulation, etc.) plus your system goals and give you a very simple materials list and some technical advice on how everything can go together from a DIY basis. They officially recommend a professional installer and offer no guarantees for DIY people as a disclaimer , blah, blah, blah.....but a competent person like yourself should have no problem executing the work. My guess is everything should cost you well under $1000 in materials - a bit more if you get the pro air cleaner as part of the deal.
I think this is a significantly more viable option for you. As always, just my .02 of course.