Both the low 3rd stage and the low fire on modulating furnaces have been tested in the field to deliver only 38% efficiency. Familiar with a consumer that had 40% higher gas bills with his 90% modulating furnace than his neighbor with a single stage 90%. In fact after 2 years he has just had it removed. Some of the new modulating and staging furnaces have slowed their blowers down to keep the air warmer which is at least an improvement.
Some new two stage furnaces are now bringing on high-fire first (wow lets produce the most heat when the house is the coldest) which is saving quite a bit more money because these furnaces don't spend anytime in low-fire.
When someone states they saved after switching from a single stage to a two stage it usually means the single stage was really screwed up by whoever installed it or your new two-stage is running most of the time in high fire and that would be good.
Sizing affects comfort more than efficiency. A furnace that is 100,000 btus versus one that is 50,000 btus use exactly the same amount of energy to heat if they are both operating at the same efficiciency. The 100,000 btu runs 50% less to heat the house.
Only those contractors that do performance testing and use combustion analyzers on all jobs would know the truth. None of them have posted here yet but they will.
Carrier Infinity is one with a new stat that does bring on high-fire first. Others have switches to jump out the staging(too many complaints).
Variable speed blowers save lots of money and are only available on staging equipment. Therefore multi-stage equipment (90% only) needs to purchased and then set up properly in the field.
Efficiency of furnaces is based more on a points system than actual testing. No furnace has ever been tested or rated in any firing rate other than high fire.