This isn't quite right. MPGe estimates how far you can drive on a "gallon's worth of electrical energy." Which is a completely absurd unit, and can't really be compared to MPG. More useful, as you said, is to know the actual electrical efficiency. A gallon of gasoline contains about 33.7 kWh of chemical energy, so 90 MPGe means each mile uses 0.374 kWh. Or 2.67 miles per kWh.I believe it means you can travel 90 “electric” miles for the cost of what it would cost for a gallon of gasoline. So, it’s slightly more than twice the efficiency of the regular hybrid mode and significantly more efficient than the ICE comparison.
Personally I don’t find it a great comparison because it’s not exactly apples to apples and there are variables here for both cost of gasoline and electricity, and you have more variables in the sense that the plug-in electric and hybrid will recover more energy from regenerative braking compared to the ICE which doesn’t do it.
In terms of true efficiency you’d have to figure out the Watts used per mile.
From there you can calculate cost per mile (using your local electrical and gas costs) or CO2 per mile (using your local electricity mix).
That mix is also why MPGe is misleading: if your electricity comes from coal, that's only 35% efficient. So if you trace the efficiency back to the source fuel, 90 MPGe might only be 33.3 MPGc (miles per gallon-equivalent of coal). Solar panels are even less efficient at 20%, or 18 MPGs (miles per gallon-equivalent of sunlight). So ... is the Prime actually less efficient?
Yes, in a way. Each time you convert energy you lose efficiency. Electricity requires converting a fuel (coal, natural gas, or whatever) to electricity, which is then converted to chemical energy in your battery, and back to electricity again when driving, and then finally to motion when driving. Gas engines go directly from fuel to motion. MPGe cuts out the most egregious of inefficiencies in the electrical system, since they're externalized.
But that's not the efficiency people really care about. They want to know the cost efficiency and the pollution efficiency. MPGe lets you calculate that, but you can't directly compare it to MPG.