Yeah, they even admit in one of the DVD bonus features that they cheated on the Jedi starfighters. Artoo's legs would be hanging out the bottom, which begs the question why not design something that an astro droid can actually fit inside in the first place? Like it was going to cost too much?

The incredible cross sections book tries to show how Artoo fits into the Naboo starfighter, and it's ridiculous.

I think the Artoo units in the Episode II Jedi fighters are supposed to be plugged into the ship all the time, and unable to run around because they don't have legs or a proper body. Not that it makes any more sense. ;)