I think you are confusing the threshold at which VAT must be collected, and my point, which is that the VAT is a tax on purchases, not earnings. VAT is collected by a vendor on behalf of the government for all sales, but has no relation to the vendor's earnings. It is a direct tax on the consumer based on the price of the good/service purchased by the consumer. Therefore, if Apple previously did not have to collect the tax for certain downloads, that benefit is received by the purchaser, not Apple. Said another way, VAT is a tax on consumers, not businesses. Consumers are the beneficiaries of this tax avoidance scheme, if we want to call it that, not Apple. At least, that is how I would characterize this situation.
That makes sense, and I see what you mean as we are benefiting from lower prices I guess. However, that doesn't mean Apple aren't benefiting too - of course they are! Otherwise they wouldn't go through all the effort to find these loopholes and take advantage of them. If Apple had their prices set higher, then they wouldn't be selling as much content as they are.