Retailers are competing with each other to offer customers great deals through Black Friday and Cyber Monday. Take Two will not be funding this, there is no reason for them to. Note, I don't have current or specific knowledge of this but I know how retailers work with video games companies!
It's $40 on amazon. It was only $34 for a little while on Black Friday. They're probably discounting it to drive up sales before the used game market picks up. They're undercutting the gamestop used game price. You tell me, what's better for TTWO, to make $34 ($40 now), or to not make anything at all and let gamestop re-sell the used game?
Not sure what you're talking about with your gamestop not having it in stock. Every gamestop in my area has it in stock. Use their website to find what's in stock and where.
It is quite possible that stores were using GTA as a loss leader meaning they just wanted to get people in the stores with that deal in hopes of selling more product on top of that. Happens all the time. And It's the store that takes the hit not TTWO.