Depending on the scope of home energy audit that you're getting you may get a heating and cooling load with that service. With this information you can then compare it to the quotes you have.
Being educated on the benefits of heating and cooling load information and then using that as a benchmark to qualify a contractor is a good step. Asking them why they did or didn't do one could also bring information into the decision making process.
A person there at your request to give you a price on replacing equipment is sometimes trained to not confuse you with details you might not understand and that can sometimes overwhelm the decision making process. Asking about those details gives the salesperson the indication that you are interested and informed and want to know something other people might not care about. A majority of the customer's they see are only interested in one thing....... how much is it going to cost.
At best, heating and cooling load calculations are well educated guesses that are designed to give an answer that is not 100% guaranteed. The information entered is only as good as what can be measured with the rest being assumed or can be closely matched a chart of norms. The dimensional data is always relatively accurate, but the insulating values of walls, ceilings, infiltration and the such are usually derived from charts of options or averages.
The decisions of what size equipment to use start with those load calculations giving the estimator a starting point. Everything beyond that requires taking into account what is going to make the customer comfortable and be as happy as possible with their decision.
I always ask a lot of questions all having to do with the customer's expectations of finished comfort when deciding what to offer as options, including the furnace size/capacity. It's not my home and it's not my call on what I think you "have to have", it's my responsibility to make sure that I offer and explain all of the options that I have available that fit your home, situation and expectations.
A 100% perfectly sized forced air furnace does not exist because the heating need of the home changes constantly. The other thing that changes is the homeowner's expectations during the changing seasons and in some cases even the day of the week or time of day. Big strides have been made with the introduction of the modulating furnaces to better fit these changes, but the comfort of the homeowner is still the driving force of what is best fit in all the conditions, situations and weather. That "best fit" is always going to be a compromise.
When considering a multi-stage or modulating furnace the duct work should be assessed also. These types of furnaces change the amount of air they move along with the amount of fuel they're burning. If you are used to a single stage (all or nothing) type of furnace you are going to potentially notice differences in how parts of your home heat when the new furnace is in the lower stages of heating. Registers in the home that are a long distance from the furnace may not get enough air to sufficiently heat the room.
Use the biggest hammer you like, pounding a square peg into a round hole does not equal a proper fit.