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.

I have successfully made strudel using puff pastry, so I see no reason you couldn't make the same substitution for your recipe. Suggested changes:

• Roll out the puff pastry sheets at least a little bit, because the pastry is much thicker than even 8 or 10 layers of phyllo. Aim for about 1½ to 2 times as big as the size you started with.
• Don't use multiple layers of puff pastry. Instead of strips, cut it into squares, put the filling in the middle, and fold it in half diagonally.
• I generally have better success making the edges stick using water rather than butter. You definitely don't need to brush the entire dough with butter; puff pastry already contains plenty of fat.
• You don't need to bother with the whole damp towel part. It takes a whole lot longer for puff pastry to dry out than it would take to prepare, fill, bake, and eat the pumpkin pastries.
• Puff pastry is much more liable to stick to the pan than phyllo, so I would strongly suggest using parchment paper to line the pan.
• The baking time will probably need adjusting, so check after 15 minutes, and keep checking periodically thereafter until you achieve the right golden-brown look.