Even with an upgrade package you would have the same problem in this case if for example the changed files included the default theme.
Yes, and this would be where reading is important. There is always a changelog that is linked in every update announcement that lists exactly what is changed in what files. If one is concerned with overwriting old files - that should be what s/he should reference.
Before WP had themes and all that, we were restricted to hacks and I used to keep a txt file on my site that listed every single file I'd altered because I'd so often been lazy and didn't read what files had been changed and done exactly what the original poster did. It happens, but there are precautions one can take.
Going back to the original post, I find it rather juvenile to come to a public forum and yell at everyone for something that, as I noted above, could have been prevented if some care with reading the announcement had been taken. The /download page always lists the latest stable, it has never been a record of what updates, etc. - that's why there's the dev blog. Which, as has been stated by other replies, did link to the single file that needed to be changed, as well as a changelog of all the other minor changes.
If you're going to have a theme in a folder "default" - it should be you, I think, that should take care to keep a backup. It's sloppy to store a theme in such a folder anyway, knowing how WP is packaged. And I've made several themes from scratch and never had a problem having them recognized - perhaps this is an issue you should research into to help avoid possible theme loss again.