Aye, I just had a back and forth with a tech rep there. They advised me at the end to contact sales to 100% understand, but the gist I got was that the FineReader Engine is $100 and it can do anything the SDK can do, but you have limited functionality in how it can operate with other programs (on Mac, all you get is Automator) and it can't be scaled to many cores. If you don't need that, then it seems to be a pretty damn good deal. Will talk to the sales rep first though.
What kind of problem were you dealing with? Were you bumping up against any constraints?