The short answer...
No, there are no significant differences
The long answer...
There are two possible things that can differ between ePods. The first is the daughterboard. There are two versions. The first has four Intel flash chips on it. The second has a single masked ROM chip. The difference is only important if someone comes up with something new to flash onto the Intel chips. I doubt that this will happen.
The second possible difference is the RAM memory speed. Earlier versions had faster memory chips than later versions. The memory of both versions is clocked at the same speed. There is no perforce advantage to either version. The distinction is only important if you want to upgrade the amount of RAM from 16MB to 32MB. (click here for details)
AFAIK, the software loaded onto the machines is identical. The various software hacks can be applied to all versions of the machines equally well.
Electronics run on smoke, if you let the smoke out they won't work