I can only describe how the temperature situation has worked out in my home.
I have my basement (where the theater, a playroom, and my office are) and first floor on one zone, and the second floor on a separate zone. In the winter, the first floor calls for heat more frequently than the second floor does (due to heat rising naturally from the first floor to the second). This has the effect of warming up the theater dramatically in the wintertime - so much so that I've had to open up the door at times to let the warm air out of the theater.
I have a mini-split heat pump in the theater, but I haven't had a low-ambient-temp kit installed on the outdoor unit, so I can't use it for cooling during the dead of winter.
During the summer, the second floor tends to call for cooling a little more frequently than does the first floor. I say only a little more frequently because my house is very well insulated (r60 in the 2nd floor ceiling/attic, and 2x6 exterior walls with r19 insulation). The theater would tend to get a bit cool when not in use in the summer if tied to the 2nd floor's heating/cooling needs, but that can be easily mitigated by the heat generated by the PJ and people during a film, and if necessary, I can make heat with my mini-split heat pump during the summer. Being tied to the first floor's heating and cooling needs has been OK for the summer months, but I have still had to augment the cooling in the theater with my mini-split during movies.
I live in NorthWest NJ (rather cold most of the winter, really hot for only a few weeks during the summer); so for other areas of the country, a different solution might very well be needed.
Sounds like your HVAC guys know how to deal with the static pressure issues that arrise when zoning isn't done properly (assuming that your air handler isn't a variable speed one - if it is, you don't need the bypass at all because the fan will automatically slow down in response to an increase in pressure in your ductwork). Just make sure that they are planning on using a pressure-operated bypass damper rather than a manually operated one. Don't laugh - I had one HVAC contractor try to pull that one on me...