How I understand it. You will have duct work run upstairs, add a compressor and lines only, run a new vent outside, and remove a chimney? Things can vary greatly depending on how they run the vents.. will they need to build enclosures to hide them or is through a closet or some other means, is your current air handler and furnace large enough for the extra two room, what brand of compressor you are getting, repairs to the outside of the house after you take the chimney down...
With all of this I feel the estimate can be low I would get everything they will do on writing, waste removal, repairs, covering duct work, electrical, permits brands of new equipment etc. The last I checked just to replace an outside compressor if it can be done will be in the 2000-3000+ range depending on who and size that is without new lines... when you have an older system and need to convert to new you are looking in the 5,000+ range and this is for AC only no duct work or furnace if needed.
Your estimate may be right or low I would doubt high but the only way to tell is to get other estimates and ask specifics and make sure all components of the new system will work together and properly heat and cool the house as spending more now if needed will save you a lot if what they are giving you will not meet your needs.