Well, I finally worked through the issues with Mail.app and mapping the Junk folder. I found the fix for it entirely accidentally – I was going through all the settings and found that changing the setting under Mail > Preferences > Junk Mail > When junk mail arrives from “Mark as junk mail, but leave it in the Inbox” to “Move to the Junk mail folder” was enough to restore the mapping for the Junk mail folder.
I also found that the Drafts folder didn’t exactly disappear, it just doesn’t show up when there are no drafts saved.
While GPGMail for 10.5 still incorrectly reports signatures as not being valid, it is still in beta and sure to improve. So, I guess the week of trying it on has begun.
Holy crap, this was driving me insane for hours tonight. I kept setting the Junk folder, and then restarting Mail.app only to see it disappear. Growl would then notify me of any new Junk mail. What a headache… I hope these go away a few weeks into the “switch” from Debian.