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Should, and yet my Smeargle keeps on outspeeding the Heatran in question. At level 68 with 0 IVs in Speed and 96 Speed, that should speed check, and it has worked before, but only two time, and the other time, the Heatran in question didn't have enough HP, and so fainted.
I'm guessing I keep getting 31 IVs in HP and 2 other things except Speed, or 31 IVs in Speed and 2 other things except for HP.
Maybe I really am just unlucky right now.

~40 times and the HP, Speed, and nature don't line up? That's almost impossible. Don't know what to tell you if you're doing it right with a Synchronizer and all though.

Strange, I guess that just because my Smeargle outspeeds, doesn't mean that the Heatran in question doesn't have 31 IVs. Or more likely, he had 30 IVs.

Still, he had 31 IVs in Attack, so I'm resetting anyways. I guess that I can only only depend on the HP checker? :/

No, at level 50, Heatran has the exact same Speed (and other stats) if it's either 30 or 31. Until level 100, you can only calculate IV ranges because they're only 100% accurate at level 100. If it has 30 or 31 Speed, then it will pass the Speed test. Is your Synchronizer in the first spot? If your Smeargle has 96 Speed, then that's the only explanation I can think of other than except maybe that your game hates you.

Are you insistent on the Heatran having your OT and ID/being from Gen 6? If you're tired of SRing, you could always trade for one.