With apologies if I am jumping in here...
Am I understanding you correctly that the ATV2 preset will play correctly in the iPhone4, iPad and ATV2?
Yes, as all three devices can take up to 30fps. However, for the iPhone4, you are wasting storage space as the file is at a resolution higher than the iPhone can display, whereas a file encoded specifically for the iPhone will be at its maximum resolution and therefore smaller.
If those are the only devices I want my media to be played on, would the only potential benefit of the Universal preset be smaller file sizes?
Yes. But you will have a file that has been averaged down, so it will still be bigger than a file encoded specifically for the iPhone, and still at a lower resolution than a file encoded specifically for the ATV2 and iPad. I.e. the worst of both worlds.
Also, will the ATV2 preset play on the original ATV?
Possibly, but not for certain. ATV2 can handle up to 30fps, whereas the ATV1 is limited to 25fps. Most BD movies, for example, are at 23.xxx fps, so both versions of the ATV would be able to play a 720p encode of that movie. BUT, the ATV2 preset in Handbrake will allow the frame rate to go up to 30fps if that is the rate on the source file - and the resultant encode will be too much for the ATV1 to handle.
FWIW, I have an iPhone 3GS, an iPad and some ATV1s. I make two versions of each rip - one using the ATV preset and one using the iPhone / iPod preset. I opt for iTunes to feed the "HD" version to the ATV and iPad, with the "SD" version going to the iPhone.