Migrating multiple blogs to multisite seems fairly complex.
running a network is fairly complex. ;) that's why it's not a one-click in the backend.
Also, a LOT depends on how your current sites are setup.
How are popular sites handling this?
Carefully? I don't know of any huge popular sites that are doing this. Many of then that needed multiple sites in one install have been using mu.
If you have to have the dns and domain in place during installation, that means you effectively have to disrupt your site for a day or more.
No, you don't You can set up the sub-blogs in your install, make sure they work then flip the DNS over. With domain mapping there are a few steps you don't need to do in any particular order, depending on results.
And what if something goes wrong?
Backups. :) And if you're worried about down time, then you do them during as low traffic time.
I'm trying to get all my blogs setup in a separate account and test it before switching over.
And that's exactly what a lot of people do. If you've got it all tested, got a plan in place, and have super sys admin skills, I;ve seen it run smooth in maybe a half hour or so.