Wow, I'm surprised nobody has answered this yet. Doesn't seem like the right section of the forum for this question... But as far as I know the answer is that an eGo is never actually putting out the whole 3.7 volts, more like 3.4 or less, but any li-ion/imr should come out of the charger at around 4.2v, maybe around 3.8 or so under load, meaning that is what the atty/carto would be getting. So yes, a box mod will "work better" than an eGo.
Also, mah = time between charges, so more mah = longer runtime between charging. Though the 2000mah batts such as I use will also hold a higher voltage for longer, as compared to a 900mah which will experience faster voltage drop.