I cannot begin to tell you how many posts I've seen with 'I edited a file in wp-admin and when I upgraded...' You're right, it should be a stupid moment. But people do it far more regularly than I could wish.
As for a theme being 'core code' ... *sigh* Yes but.
You can't run WordPress without A theme. In order to have WordPress run out of the box, a theme must be included in the install. Yes, WordPress COULD make multiple packages, with and without a theme, but in order to make it the simplest method possible, they decided to just include it in the, singular, package.
My personal feelings about a theme (and a pair of plugins while we're at it) being included in 'core' aside, the fact is this: Twenty Ten is going to be updated every time you update your WordPress install, so do not edit it directly.
If you want to post to http://wordpress.org/extend/ideas/ to pitch it as an idea, go for it, but it's been like this for 5 years, and my gut feeling is it won't change. This is a far more complex situation than I'm making it, too.