The Athas dot org published supplements follow the 1995 - 1996 canon and retcons slavishly. 4E was a reset to the original setting. See what the designers thought about it here.
4E Dark Sun had no alternative energy sources. It was one of the things that the 4E team wisely dropped. In regards to how 2E alternative magical sources should work in 3E/3.5e, its important to remember that these are different game systems and implementation is thus going to be different. That said, the Athas dot org implementation is reasonably accurate to the 2E presentation of the alternative energy sources. The problem is that the alternative energy sources completely overturns the premise of the setting. I am confident that had TSR not gone broke, the alternative energy sources would have either been retconned out, or severely nerfed. As it is, we had to wait for 4E for the alternative energy sources to get the axe.
I think we can accommodate the alternative energy sources, but not as they stand as present. Right now these alternative energy sources warp the setting. I give a narrative example here.