Note that the stop on the D and N is called Pacific, not Atlantic (on the Q it's called Atlantic). But it's all the same station, and it is indeed connected directly to the Flatbush LIRR terminal.

The D and N are express in Brookyn, and therefore probably a little quicker than the Q.

I agree that it's a complete waste of time to go to Penn Station. Even if you have to switch in Jamaica to get from Flatbush to your LIRR destination, the change in Jamaica is usually quite painless.