I don't think there is anything in the phrase "Right on, commander". As others have said, it's just a nod to the old Elite game.
I have been looking at the holofac message text again. Repost:
"The video played.
"If you're listening to this it means your smart enough to have bypassed Galcop, Federation, and Imperial security." The woman on the video smiled. "Not bad, but it's nothing compared to what's coming. I'm guess you'll be pressed for time so I'll be quick. You'll find the co-ordinates at the end of this message. You'll need a tough ship and a good pilot. It's a long way, so make sure you're prepped, no one will be around to help you out. Once you reach the rift you're going to have to plot a way across. There are no stars for dozens of light years and the dark systems haven't been mapped, so take your time, watch your six." The woman leaned in closer to the recording device. "What's there? Wish I could tell you, but they edited my memory pretty good, took me long enough to stitch this lot back together. Whatever it is, it's something that Galcop, the Imps and the Feds don't want us to see. Good luck, and ... right on, Commander." The holofac faded, leaving them with just the text."
What about if the actual message ends with "watch your six", not "right on, Commander"? To me it seems everything after "six" is a comment on the message itself. That last part doesn't add anything new, nothing on the rift or what is there, just the comment that the actual info was hard to remember after her memory had been edited.