maybe I'm just ******ed and don't understand exactly what the OP is asking or what that link to google's forum is talking about but...
what I'm experiencing is that when i read an email then mark it as unread on my computer, my droid will recognize that action (i.e.: marking it as unread) as a new email and give me a notification. This happens with both my gmail and yahoo accounts and doesn't really bother me at all.
I also get a few email notifications for my yahoo account but no new emails are shown in my inbox on my phone, but when I check from a computer, there are a couple of new ones in there. However, with all of the known POP email issues this phone has, I was never really too concerned with this. Hopefully it gets fixed in the next OS update, but whatever...