But why didn't they give the WR the same 48mm front forks like the YZ. They kept the 46mm instead .
This is an easy one. They have a warehouse full of 46mm forks, they need to get rid of them, but they also need to improve them. They clean out the stock by coating the fork legs, and selling the stock off until the next years model, or till supplies are deleted. Also, the WR really doesn't get as stressed as an MX bike, so the 46's do just fine with the slight improvements. Should have asked me last week when you were over.
Only reason I claim to know this is because that's how the business I'm in runs. Leftovers just collecting dust doesn't do anything for the company, but repackaging it and clearing it out will get someone a nice bonus.