I'm far from experienced, but here's my point of view. If a Mega changes a Pokemon such that its tier should change, the Mega Stone should be placed in the tier the Mega Pokemon would be tiered in and the Pokemon should be placed in the tier it would be tiered in without the Mega. If Absol is RU-worthy and Mega Absol is OU-worthy, then you can use Absol in all tiers RU or above and Absolite in all tiers OU or above; putting it on Absol is a logical choice, but I'm PRETTY sure the Gen V OU Soul Dew ban bans Soul Dew on non-Eon Pokemon, which is the closest precedent Smogon has, so we can't allow Absolite on random Pokemon in tiers below OU in this scenario, just to avoid random Trick chains and stuff. If, say, Pinsir is RU-worthy and Mega Pinsir is NU-worthy, then we would put Pinsir in RU and Pinsirite in NU; you can USE Pinsirite in NU, just not Pinsir, so it's hardly of use. But there's no way of using Pinsir in NU that FORCES you to use Mega Pinsir and not normal Pinsir, so it has to be done.
If people disagree with me, they're probably more right than I am. It's just that the differences between, for instance, Mewtwo and Mega Mewtwo X, or Charizard and Mega Charizard X, or ANY Pokemon whose role-switch is significant between normal and Mega Evo, seems so dramatic that it would be odd to tier them as one Pokemon. We've done it for Soul Dew, we've done it for Rotom, Shaymin, Deoxys, and Kyurem; why can't we do it for Mega Stones and Mega Evolutions?