I have to start with a correction to your statement: being in OU DOES NOT mean that a Pokemon is too powerful for the lower tiers. Usually this is the case, that is true, but it does not necessarily have to be that way. To get in OU the Pokemon simply has to be used enough. That's why it is called OverUsed. It is the Pokemon that are used a lot.
The BL (or BorderLine) tier exists for the Pokemon that ARE too powerful for UU, and so have been banned from it. They aren't actually used enough for the OU tier, but are considered unfairly powerful in the lower tiers, hence they are stuck in BL, unless their usage goes up to the point where they can move into OU.
The discussion of how the tiers work is important, because when it comes to Charizard, the regular one is used a lot because it has 2 very good Mega Evolutions. However, even though it almost always uses a Mega it always starts out the battle as a regular Charizard. But because of the Mega's, it is used enough that it is in OU, since it is impossible to use (for example) Mega Charizard Y without having a regular Charizard first.
So you send out your regular Charizard first, and the Mega evolve it later. But the usage statistics don't care if you are mega evolving Charizard - it sees a Charizard in play, and goes "another score for Charizard!"
Some Pokemon get their Mega stone banned from a certain tier, because they are considered too powerful (e.g. Mega Kangaskhan or Mega Lucario from OU). The base Pokemon is not banned, however, but because the Mega is the usage stats for the base form drops off in subsequent months, and so the base form is dropped to lowerer tiers (I think Lucario is UU at the moment, and Kangaskhan NU), but their mega forms are considered Ubers.
I hope this slightly long-winded explanation helped.