If it's going to force an automatic scan—and I would prefer that it did not—it should be limited to the system Music/Photos/Videos folders.
Like I said... I'm not a fan of the countdown.
However, the fact that it looks beyond those folders is, I think, quite important for "novice" users who might be squarely in the target market for MC. For example: People coming from iTunes because their media library is too big, so they had to move it to an external disk, and iTunes is behaving badly (which it does with large external libraries).
Sure, you can redirect those system folders to point to your external disk, but how many people do you think figure out how to do this and will have done it? The idea is to just find your stuff. If it finds stuff you don't need, it isn't a big deal, just delete them from the Library. But forcing people to understand the filesystem and where things are stored (like all of us do intuitively) in order to even get their stuff imported is, for some people, a major hurdle.
The idea is to make it simple to find all of your stuff. So, it tries to find all of your stuff, in the places where people usually stick it, without also grabbing a ton of irrelevant system files.
We're nerds, and we might not want it to touch certain filesystem areas because we use those for "special purposes". I certainly don't use, myself, the automatic first-use scan. But, I
do think this is something far more likely to annoy people who can already handle it (us power users) than those who really need the help. Most people, I'd guess, would rather it just Find My Stuff and move on to actually using it.
But, I agree, and have agreed from the very beginning, that it should ask, not just countdown and do it. I think offering the First-Use Scan in an Action Window with a Yes/No that doesn't dismiss until you respond to it would suffice.