Oil Overfilled - Is it really a big deal??

Ok...so I took my car to Central Florida Toyota for it's first two oil changes. I supplied the Mobile 1 5-30 synthetic.

The first change was overfilled - and when I first mentioned this to the service advisor, he told me "It is like that until all the oil drains down, then the level would be right" - I asked they take the oil out until it is at properly at the full mark - they were very polite and did what I asked, but always maintained that putting 4 quarts in will cause no damage and is proper.

My second oil change, their 'prius master mechanic' did my oil change and balance/rotate the tires at the 10K service. Again, I found the oil overfilled. The mechanic said the Prius actually takes 4.1 quarts - but he only put the 4 quarts I brought in. Again, I asked the level be lowered to match the full indicator on the dip stick. Again, they were very polite and did as I asked, but again said that it would cause no damage and is appropriate.

So my question is this....Am I making a big deal out of nothing? Am I wrong about the overfilling being bad? - the owner's manual does clearly say overfilling will cause engine damage - and 3 - Why in the world did the Toyota engineer's not just inlarge the oil pan ever so slightly to hold a full 4 quarts to make this a big non issue?

Thanks!