Products in the factory stores are made specifically for the "factory brand." The quality is not the best and you will often times find some form of J. Crew embroidered logo on the polo's and some other items which you would not find in the mainline stores. If you are looking for cheap, disposable shirts, etc. the factory store is ok but if you are looking for long-term wear I would look elsewhere.
PS I'm a sales associate/men's personal shopper for J. Crew so if you have any questions about anything let me know and I'll do my best to help you out.