It might be because Apple has a tendancy to fallback on Apple Script to do repetitive tasks...you could create one that opened all the files in a folder and after setting up an output setting, use that one to do the conversion. I always used cleaner to do batching, much like I used Debabelizer on stills long ago. Compressor just doesn't have a friendly interface IMO. Same with iTunes...seems Apple could have built in an export module for that rather than use the playlist model. But them it might look like they were encouraging us to use iTunes to make copies and make the exporting easier.
Not sure, but QT is still pretty robust with the Pro options, and if you don't have too many files you can open one, start an export, open another and start another export and so on. Not quite batching, but multitasking!