This would <snip>.... also reduce the tokens available to the user later on

The more I think of the typo and the explanation about it in that article, the more unclear I am about that whole code.

Keeping aside this hack, for a moment, if that is indeed a typo and instead it should have called the lower case transfer method to really reduce the user tokens, then does this mean that all these DAO contracts (or whatever the right term is) that have been executed till date have been affected by this and as such the entire eco-system state was already messed up before this hack?

Nothing in that article suggests that this code flow, where this apparent typo is present, is applicable only for this specific hack.