I definitely agree with your first paragraph: Machamp is a powerful Pokemon capable of haxing his way through most of his checks in the tier and/or defeating them with coverage moves, and anyone building a team needs to consider that. (He does have a few counters outside of physically bulky ghosts, though: Slowbro, who's already been mentioned, only loses with significant hax and prior damage [Toxic won't kill him fast enough]; and Weezing, who can handle any of his typical attacks, but who lacks recovery and perhaps enough of an offensive presence to do anything but burn Machamp.)
But I don't think Payback is useless (although I could see why it might be on the sub set you're using). Let's take Mismagius as an example. On the switch-in, SubCM Mismagius takes 66.3-78% damage from Stone Edge or from Payback. So if you predict well, they're equal in that regard, but prediction works both ways: what about when Missy switches in on your Dynamic Punch? Well, Stone Edge still only does that much damage to her, and has a good chance of missing (a chance which can be exploited if your opponent knows you have that move, and fishes for a miss by subbing), while Payback cleanly OHKOs her. An unboosted Shadow Ball 3HKOs most Machamp, however (32.3-38.1% on its lead set), making the difference between choosing Stone Edge and Payback a difference between losing one-third or two-thirds of your life to take out this check (or all of it, if Stone Edge misses just once). Behind a sub, this might not matter, but on any other Machamp set, I'd argue that Payback is extremely viable, reducing the list of ghosts who can check or counter him down to Chandelure (I guess: I'm sure one of its set can OHKO him) and Dusclops.