Because with JUST an ATV App, you may decide to forgo further services from Comcast AND/OR decide to just use ANOTHER TV Streaming App. With having you subscribing to THIS service and Box, you feel that Xfinity gives you everything and will stay with them. With a physical product in hand and their Voice Remote, you [they hope] will love the experience it gives you. with just using Roku/ATV/FireBox/etc, you can more easily drop one tv service for another without caring about the experience since you are using the alternative Streaming Box.
This is similar to Starbucks and K-Cups. Originally Starbucks was NOT selling them. Why? because making you go to THEIR store gave you the experience they wanted, even though they were selling Coffee Beans in stores. The idea was the experience of grinding or at least smelling the coffee before you brewed it...the experience. with a K-Cup, you are in it for speed, not flavor...and you may think it wasn't as great as the Starbucks Store coffee and decide to switch to another K-Cup. BUT, overtime, Starbucks realized selling K-Cups still brought in money. so, perhaps one day Xfinity will just let you subscribe to their Xfinity FLEX TV App but until then, they want to handle the experience.