There are several types of efficiencies. The efficiency on the yellow "Energy Facts" sticker on new HVAC products is AFUE, Annual Fuel Utilization Efficiency. AFUE Factors in start up and shut down losses, off cycle losses, to give a total percentage of how much heat is provided to the structure versus how much heat the fuel consumed contained in ideal combustion. AFUE is the most useful gauge of fuel use, but does not factor in electrical consumption of fuel burning equipment. Nothing I have seen published accounts for electrical consumption.
The efficiency printed out by my combustion analyzer is combustion efficiency. This has nothing to do with how efficiently the heat exchanger transfers heat to the building. It does not factor in start up and shut down losses, or off cycle losses. We can have 80% combustion efficiency in a gravity furnace that has an AFUE of 55%. It burns cleanly, little soot, just enough excess air, but is still an energy hog. Also, your new 95% AFUE, tax credit condensing furnace tests on my combustion analyzer at around 90% efficient. The reason, the analyzer does not account for condensation. To truly measure efficiency of a condensing furnace we need to measure condensate produced.
Another efficiency you rarely see stated anymore is "Bonnet Efficiency," also called "steady state efficiency." Furnace Data plates list an input capacity and output capacity, some easy math gives you a percentage. Example, a natural draft gas furnace with 100,000 BTUH input, 80,000 BTUH output has a bonnet efficiency of 80%, but an AFUE of only 65%. After it heats up to temperature, and before it shuts down, its 80%, but that natural draft is removing heat all the time, even when the furnace is off.
Generally, gravity boilers and furnaces are 50-60% AFUE.