It's likely that Apple is just forgoing the input tax credit in this case. They remit the GST on their sale and because they aren't charged any GST by the app creator, they don't look to offset.
Now, the major issue here is that if the app creator is making $30K+, it is THEIR responsibility to charge GST, which means that if there is no mechanism to charge in addition to the price, it's automatically inclusive. The CRA doesn't care how you collect the tax you owe, they just care that you pay it.
For a vast majority of app creators, $30K probably is a target they are on the lower side of, but I'd imagine people making a living on the apple store, the GST is coming out of their revenue directly. At least, that's how CRA would look at it.
Now that being said, CRA might be treating this entire industry as an undefined gray area for the time being, particularly since they are getting the GST on the final sale by apple, but I don't think that will last long.
