I'm pleased to announce that as of now, After Dark episodes for a show are included in the 5by5 Time Machine feed for that show. Instead of creating new, separate feeds for the combined show + After Dark, I figured that if you're a fan enough of the show to want to relisten to it, you'll probably want the After Dark too. And since creating a separate feed would require people that wanted them to resubscribe to that new feed, I thought it would be a big hassle to put everyone through.
That said, if you really don't want After Dark shows in your show feed, just append ?afterdark=no to the feed URL, like so:
From a technical standpoint, the ?afterdark=no parameter filters out all episodes in a feed that also appear in other shows. For regular shows this filters out episodes that appear in the After Dark feed, but as an added bonus it also filters out episodes in the After Dark feed that appear in other, regular shows:
The above feed returns only standalone After Dark episodes. They're not frequent, but occasionally Dan will post things to the After Dark feed that don't really fit in any other show, and the above link is a great way to subscribe to them. The "0" in the URL means that this feed has no delay, so you'll get the episodes as they come out.