Can I substitute store-bought puff pastry dough for phyllo in pumpkin pastry?
Looking at this recipe I don't see any reason why you couldn't use puff pastry as the container.

The only ways that the preparation would be different is:
puff pastry doesn't dry out as fast as filo so you don't have to worry about the wet towel in the instructions.
You wouldn't want to do multiple layers of puff pastry as the recipe calls for. You would just form a single pouch to hold your filling and seal it well.

Know that the texture will be different of course. The filo will be a bit more crisp and the layers larger and more distinct- filo is also a lot more work. You may find that the baking time needs to be adjusted a little but I don't think it will be very different if at all. Cook them until they're golden using the recipe's time as a starting point.

This recipe is in a Mediterranean style and filo would be more traditional but puff pastry would produce something tasty.