Yes, Gunrunner is primarily shotgun-specific, and yes, Shottyhead could probably do with a re-tooling/buff, but I don't think making Gunrunner the shotgun mastery is a good idea.
For one thing, I'm not sure that you're correct in writing off pistols as non-synergistic. I've never tried DG/MGr, but free shot every move is better than free shot every dodge; the question is whether it's worth losing the free reloads over this advantage.
To be completely honest, I've always seen Gunrunner as borderline overpowered (specifically, the combination of Gunrunner and Shottyman). 45 turns of bottomless clip blitzkrieg action is kinda silly, the only significant drawback being that it's EXP-intensive. However, if Gunrunner must be buffed, just have it work in conjunction with rapid-fire weapons (which a general trait arguably should).
Finally, a single mortem really doesn't mean anything with regards to a trait or a build. If someone posts a successful fists-only N! run, that doesn't make fists-only a good strategy, it means that the player who did it is exceptionally good at the game (and knows how kill attribution works). In this particular instance, you've essentially said "I struggled using a HMP Explorer build in UV Conqueror, therefore Gunrunner is underpowered". Even if you did really well with that build and beat the game, that wouldn't show that the build was good, it would show that you're good.
W/r/t the tangent, you can ask the wiki about knockback mechanics rather than speculating. Shotguns deal knockback if they deal at least seven points of damage.