There is actually quite a lot of difference between the two. Regular whole wheat is made of "hard" red or white wheat, is higher in protein and in gluten. It has a coarser texture, and is great for making yeast breads.
Whole wheat pastry flour is made with "soft" white wheat, is fluffier and softer in texture, and is lower in protein and gluten. It has the best texture for quick breads like muffins, pancakes, etc.
You can make pastries with regular whole wheat flour, but the texture will be much, much better with a fine milled pastry flour. You can't really use pastry flour for yeast breads, as there isn't enough gluten for a good rise.
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