Those deals are never done with cash payments, the most likely "payment" was MS-paid marketing & lower licensing fees, maybe instead of 30% it's 10% (that percentage is just an example, we don't know the exact percentage), the lower licensing fees could possibly apply to all SE-published titles within a certain window, not necessarily just TR.
Hmmm... Well, I doubt MS is in any position to be charging royalties anyway, given the state of their hardware sales on a worldwide scale relative to their competition. They'd probably be on the verge of getting abandoned hard by third parties like Nintendo did/has... which is why it's quite the mystery to me how Sony wasn't killed off during PS3's cycle. I'm guessing Sony was suspending royalty fees carte blanche just to keep third party support in those days, so it wouldn't surprise me if that's what Microsoft is having to do these days.
So yeah, I think actual, real, hard, fiat currency is being used to secure these deals, maybe even with stock/shares to sweeten the pot. Shit, I know if I were a developer/publisher and Microsoft wanted to pay me with stock, I'd make Call of goddamn Duty exclusive to them, for the right amount. Turn my ass into an investment banker overnight.
Like, I'm honestly just surprised why Microsoft isn't buying off all the third parties right now? They have tons of stock. Why stop at tomb raider? Cuz of consumer backlash? Nah. Consumers don't know what they want unless you tell them. That's why you keep purveyors of echo chambers like Kyle orland or whatever around.