I think either or works fine. I know some people cut a small hole in the cage and hook up one of those all day feeders (I think thats what its called ) so it's faster/easier to feed the buns. I usually give my preg does a big enough dish or use a all day feeder so that she can be free fed.
If you put a bowl / crock in with most of my rabbits, they think they've got another frisbee to sling around. I've only got 3 rabbits that will leave food in a bowl/crock without slinging it around
Since I raise Angoras, my rabbits always run the risk of getting wool block and one of the primary signs of wool block is loss of appetite, so I like to be able to monitor who's eating and how much. I use a small crock for each rabbit and they get a measured portion of food at night, when they're in their cages. It's almost always gone in the morning, but if it's not one day, I know I should keep an eye on that rabbit. While most breeds don't run the risk of wool block, loss of appetite is still an early indicator of illness; for that reason, I don't really like the idea of auto-feeders. It could be days before you notice decreased consumption and start monitoring the rabbit.
I free feed hay all day and night, plus they get two servings of wild forage/organic vegetables from our garden. I can't really track how much each rabbit eats of free-fed foods (our rabbits are raised in a colony), but the pellets are easy to watch.
I've never had a problem with any rabbits throwing their food bowls. I use shallow ceramic bowls (mine are actually not even made for animals, they're from the kitchen section of a Target store) and though they sometimes get moved around the cage a bit and every now and then someone tips one over, it's a very minor issue.