Hi!
G3.1.2.1 is pretty clear that for the baseline model you're supposed to use the minimum equipment efficiencies shown in Section 6.4. In other words, the single zone gas furnace you reference would be baseline-modeled per Table 6.8.1E, so a small gas furnace (<225 MBH) would be 78% AFUE.
So your equipment EEM in your design case would be the 94% furnace.
The only way I know this is because I'm working on a building with 6 of these little guys.
Good luck!
MARK DARRALL, AIA, LEED AP BD+C, NCARB