The base Model Y (RWD long range) is comparable in features and performance to the RWD long range Model 3. When you compare those two, it's only a 4K price differential (47K vs 43K). It's a bit misleading to say the Model Y has a 13K premium over the 3; that's only true if you compare two cars with drastically different feature packages.
You're forgetting the tax credits on the Model 3, which probably won't exist when the Model Y is released. This is also an important factor for the future because the price of the Model 3 will likely be lowered as the credits expire.
It is misleading because it is a very specific case in California/US. For people in other countries these things don't apply. We have 10k euro discount to Electric cars for instance. It would apply to both cars equally.