Basically they are simply two different ways to call into the external applications to read the data using slightly different technologies - applications can be inconsistent about not working with one or the other, but in most cases they'll work with at least one. Our recommendation is to try javascript first (it's generally a bit more efficient) and if that doesn't work, try UIAutomation. 
 

Totally unrelated to your actual question, I'm seeing over a dozen links there - did you paste those in and then delete them from the post? You can make those go away by editing your post and clicking the x button next to each of them, I just want to confirm they didn't show up in some other unrelated manner.