Think about it this way...the KF guys were at THE gaming media powerhouse website. They learned how to produce content in a world where they had the best equipment and a large team around them. If you believe them, which I do, they now struggle to get out 18-20 videos per week, half of which are shorter edits of a longer shoot (GoG Show and KF Gamescast).
Partnering with a group that started small and has grown into the type of organization they probably see themselves as five years down the road gives them a lot of insight into how they can break up their responsibilities and improve their workflow. It doesn't mean they'll ask Rooster Teeth something like "What content will propel us forward?" Rather, it seems more like they'll be asking Rooster Teeth "What can we do to get more of our ideas into production?" If you're a fan of Kinda Funny, or any small production company for that matter, I imagine that second question would appeal to you quite a bit.
In exchange for that advice and mentorship/partnership, they're joining the businesses in a model that's already similar to how Kinda Funny operates. They use a third party store and ad sales company today already, but they will now use Rooster Teeth for those functions. They've basically invested in one another and it's in both companies' best interest to grow Kinda Funny in a way that will keep them successful and true to what's brought them this far. Alienating fans means less Patreon money, fewer merch sales, and less views which hurts the income of Kinda Funny AND Rooster Teeth. If they work together to grow sensibly, everyone wins.