That's not the the point: the point is how we view the mega stone in relation to the base Pokemon. If you don't have an issue with banning a Mega Stone and not banning the base forme with it, then it doesn't really make any sense to me why you oppose allowing say Absolite in UU and regular Absol in RU when it's really no different then Absolite being BL and Absol being RU.
Because this logic doesn't work in the reverse, ie when the base Pokemon is used more with other items than the mega stone. So there is zero possibility of there being an option of Absol in UU and Absolite in RU. The option is there to just do that, but it's a nonsensical one.
Our current model tiers Pokemon/items/abilities/moves based in absolutes, for argument's sake let's say: Absolite is BL because it was determined that megaevolving Absol into Mega Absol was too much for UU, but base-forme Absol was determined to not be broken and therefore was not banned along with item.
Changing to the new proposed model does not tier Pokemon based in absolutes, instead based on intent to usage as per Antar's OP, and on an indefensible argument of the inability to tier the mega stones below the base forme.
Our current model is the more logical one since, as Aurora just pointed out, you cannot have the mega without the base, therefore, the base is the one that should be tiered as it falls in line with exactly how our usage-based model is set up. There is no contradiction if you view the Mega Stones as items; powerful items that affect some Pokemon extremely drastically, but simply items nonetheless. If you do that, then our current model works exactly as it always has, ie tiering Pokemon based on usage and banning items when they are proven to be broken.
Finally, and unrelated to Spirit's post above, is that there is no way that I can allow Pokemon to be dropped into random tiers based on "educated guesses." That throws our entire system of objective tiering out the window just to appease those people with no patience. We have the quick drop system available, just use that.
EDIT: and also, I have to laugh at the "our tiers can change drastically based on the whims of upper tier usage" when A, there is no escape from that even without this change and B, this can happen at any time due to the whims of GameFreak as it happened in BW. Sableye suddenly getting Prankster and Alakazam Magic Guard threw every lower tier into flux, and other HA releases did as well.
Our system is most effective based on an objective usage-based criteria as DJD and X-Act created and proved years ago. Unless we move away from that, the upper tiers are always going to "intrude" upon the lower tiers in some manner based on the metagame trends that happen in the upper tiers along with new items/Pokemon/abilities/mechanics that happen mid-generation due to GameFreak and other events.
So that last argument really just boils down to: tough shit, deal with it.