Yes, it is a bunch of baloney.
Doing the heat loss you used a design outdoors temperature that you probably rarely experience. The furnace needs to be sized to keep your home at its design indoor temperature (usually between 70 and 75 degrees) in the most severe weather. Since that design of most severe almost never happens the plain truth is that for most of the time your furnace will be oversize and often considerably oversized.
The best furnace efficiency is gained when the furnace is running constantly.
The idea behind the two-stage operation is that most of the time the furnace will be firing on the first stage which is about 70% of its maximum firing rate. Even at this reduced firing rate the furnace is going to cycle on and off to maintain the indoor temperature at the desired set point. It will however be firing for longer periods so the efficiency will be higher than if it gave a shorter cycle.
With the two-stage option you can maintain a closer temperature differential and this will result in greater comfort.
The variable speed is a term that only applies to the blower. (There are some modulating forced air furnaces but they are pretty rare and usually only in larger sizes.) Specifically, instead of having only three or four selectable speeds for the blower the variable has a multitude of selectable speeds. These speeds are determined by what the furnace is doing and also during the original installation.
For example, if you have the "Fan On / Auto" switch selected to "Fan On" the blower will run at a very slow (and quiet) speed to maintain a minimum air circulation through the ductwork and your home. This can give you much more comfort and even temperatures in addition to continuously filtering the air. When the thermostat "calls for heat" the furnace will light on the first stage and the blower will "ramp up" in speed to a higher setting to maintain a specified temperature differential across the heat exchanger and "push" the heated air into the living spaces. If necessary to go to the second stage of heating the blower will ramp up to a higher speed so the speed of the blower is always in close control of the furnace operation.
All that said, the installation of furnaces has become even more of a crap shoot because the sales people no longer need to closely ascertain the necessary size for the particular home. The tendency is to simply install the two-stage with the same, or even higher, BTU rating as the original furnace. I found this out the hared way. My original furnace had a 60,000 BTU rating and it was oversize. I went with the smallest size two-stage variable speed furnace available form Lennox and it was rated at 70,000 BTU. After signing the contract and after the new furnace installation I looked at the nameplate and discovered that a substitution had been made and I had a furnace rated at 90,000 BTU.
That's 50% larger than the original furnace!
I called the salesman and his explanation was that this way my furnace would never go to the second stage except when the outside temperature was below zero. Only problem is that in the 57 years I have lived in the greater Seattle area the temperature has NEVER gone below zero. I had received a furnace with the first stage more than 10% larger than the original furnace and it had the very real probability of operating at 50% more than I needed during the coldest weather.
I made the installer come back and install the proper (and contracted for) size furnace. I think the reason for the initial furnace being installed was that it simplified the duct connections and the contractor didn't give a darn that the BTU output was way in excess of my needs.
So, DO NOT let anyone talk you into buying / installing a furnace larger than your heat loss calculation shows that you need.