Times may have changed, but not all that much. More to the point, the studies quoted by the ACE optimistically weight their energy estimates on recent relatively high crop yields. And while genetic tinkering and hybridization do help improve yields, they still don't affect crop yields nearly as much as the weather. And the weather can only be taken into account by looking at old and long term data equally with recent data.
Also, I prefer the ethanol study I use because it is the only one which explains its methodology and the reasoning behind it's net energy calculations.
Finally, it still yields a positive net energy balance. And a conservatively calculated one. I personally prefer conservative methodologies to optimistic ones because once you turn the study into an actual real world implementation, it's always better to be pleasantly surprised by real world results than unexpectedly disappointed by false hopes.