I would imagine that Merlin Studios runs as a separate company and charges the price it does to the parks purely for tax reasons.
The park's pay a certain percentage of tax on all profit and that tax band is higher if the profit margins are higher. If some of this money goes into Merlin Studios instead, then that tax isn't being paid, but the money is still going in to Merlin. I'd imagine there's an element of being able to claim back VAT on Studio products, too, but can't be 100% on that.
So imagine that you have 1 business earning £1 billion and paying 40% tax on it's profit, your second business is earning £200 million and paying 25% tax on profit. The threshold for the 40% tax is £700 million. So business 1 pays business 2 £300 million for something. Both businesses then pay 25% tax. Business 1 suffers and business 2 benefits in terms of figures, but seeing as they're both owned by the same parent company, the overall business benefits, especially in terms of stock market value.
So, yes, it is all about money, but I wouldn't look it at from a purely negative perspective. It's something all companies do, and as long as the actual cost of the studios involvement is in the initial budget for a park development, then I don't really see what the problem is.