I agree that this can be confusing, but it's helpful for external links. I'd rather have a user be confused for a minute than have them completely forget about my website. Not to mention, when you close the new tab you'll probably end up looking at the tab containing my site again. At the end of the day, it's a usability vs visibility tradeoff.
> Don't have an FAQ page
Do you really think most users don't know what a FAQ is? Unless your target audience is 12 year olds I really doubt this is true. I do agree though that having a separate page for your FAQ means your workflow is lacking the proper information users are looking for.
> Don’t give table rows highlighting mouse-overs if the rows aren’t clickable
Totally agree. I think this is the biggest thing Twitter bootstrap gets wrong. Sure it's easier for lining up a row, but if you use zebra striping that won't be an issue.
When you say "I'd rather have a user be confused for a minute than have them completely forget about my website" you're essentially saying that you'd rather the user have an unpleasant memory of you than no memory at all. That seems like a pretty shallow notion of branding. I'll never forget ExpertsExchange, it doesn't mean I ever wish I still had to visit it.