Why wall them when they wear themselves out so quickly? Toxic Spikes is perfect for this, it just doesn't work on things that fly and mix attack. You can also use Sandstream, but that weakens Cresselia, one of the best mixed walls. Sure you get Shuckle, but meh.
Anyways, how did you find out that Magmortar got Mach Punch? Only problem with that set is that it is still walled by Blissey. Do you use Thunderbolt for anything besides Gyarados? 2 fighting attacks seems lame, but meh.
When I found out Typh couldn't get Mach Punch, I looked up the pokemon that did. Since I didn't want another lame Infernape set, I decided to try my hand at Magmortar. I was actually surprised our Smogon analysis didn't have a Life Orb set.
Anyway, Tbolt in useful for Water and Flying (respectively) in general since it packs a punch without any real drawback. The set admittedly can't do much to Swampert, Garchomp, and Blissey, but Blissey is setup meat for many pokemon. Hovever, if you try to counter Magmortar with something that doesn't resist Overheat (and isn't Blissey or SD loaded Snorlax), you've just lost yourself a pokemon. This destroys the bulkiest Bulky Ground, Hippowdon, with ease ands by implication also slaughters anything else (Gliscor, Donphan).
Mach Punch is more of a teching move than a mainstay attack. Its good for finishing off weakened pokemon that are faster than Magmortar. I'm not going to waste time on a LO set coming up with a way to kill things Magmortar can't kill short of a Focus Punch to the face. (which still doesn't OHKO Blissey or Snorlax without more attack.)
Theoretically you could replace Mach Punch or EQ with Focus Punch, but my experience has been that EQ is an extremely useful gap filler (without the obvious drawback of playing chicken with Focus Punch). Cross Chop is unfortunately incompatile with Mach Punch on the same set.
Anyway: LO Thunderbolt on various (non-Swampy) water or flying pokemon:
Max HP Max Def Bold Suicune: 64-75%
Max HP Max Def Bold Milotic: 61-71%
Max HP Max Defense Bold Vaporeon: 65-76%
Max HP 128 SD Modest Slowbro: 76-89%
Max HP 128 SD Calm Togekiss: 56-66% (Overheat: 62-72%)
In other words, you don't want to switch in on the wrong move because you
will be hurt. If the opposing Bulky Water is weakened, Thunderbolt is likely going to finish them off. If they switch in expecting Overheat, their lease on life just got shortened.