Does Pella manufacturer the same quality door in their catalog for Lowe's that it produces for pella distributors using their name?

Yes - The quality level of the products are the same no matter where they are sold. However, there may be some differences in features available on those products.

The big difference is in the quality of the services provided by the various distribution channels. The Pella distributor/window store may include several extra services that just are not available through a big box store. There is also a significant difference in the knowledge of the Pella distributors vs. an associate in a big box store. Don't discount these differences - it can cost you handsomely if, for example, measurements aren't correct or a product is installed incorrectly or placed in an inappropriate application.