Of course that will open the market for 3rd party batteries, cutting into Apple's revenue stream. Which is why they did it that way in the first place. By now, though, I should think their market is set firmly, and they can afford to take this hit. The re-engineer shouldn't be a big deal, if they decide to kowtow to the EU's demands.
The EU sure does seem to make a lot of demands that a confederation has no business making. Most of them seem okay, but it seems weird that they would exert that much influence on the tech market.