That you don't see the consistency in Amy's argument here makes me think that you misunderstand what she's trying to say.
Comparing version 1.0 to competing entertainment products of a similar price puts 1.0 at a disadvantage because it does not hold up well. In an apples to apples comparison, when compared to other MMOs at a similar price point, version 1.0 still lacks a feature set and content that other MMOs have. The only draw is the current user base who have already invested time into the game as well as people who like the Final Fantasy brand. Therefore, in choosing how to spend their money, it's likely that most people (current users and potential new users) will choose to spend it elsewhere. In this situation, it's arguable that a lower price point may help to draw in new customers and retain old customers. Or not. Who knows.
Comparing version 2.0 to competing entertainment products of a similar price puts 2.0 on more competitive ground because it should be a much more substantial game. In an apples to apples comparison, when compared to other MMOs at a similar price point, version 2.0 will have a feature set and content that should be competitive with other MMOs. If everything goes according to plan, it will have its own unique characteristics that have a better draw than other MMOs, in addition to benefiting from the Final Fantasy brand. Therefore, in choosing how to spend their money, it's likely that a higher number of people will consider version 2.0 a better value for $12 than version 1.0. Additionally, in choosing how to spend their money, a consumer might opt to choose FF14 version 2.0 instead of a more established MMO because of the things that FF14 version 2.0 might do better than other games like WoW of Rift.
It's all about assessing the market environment in any given situation and then trying to predict what consumer behavior will be.
Right, we don't know if $5 is the perfect equilibrium point of revenue maximization for sure. Just as we don't know if $12 is the perfect equilibrium spot as well.
If you concede that the argument as laid out in the OP "might be right", then that's pretty much all I was asking for: That "the concept of lowering the price would be more beneficial to SE" is plausible, and should be considered by management.