You get the extra villagers instantly once you get your TC up. You get the villagers, albeit delayed by a 2 minutes, so it only makes sense that you get the resource penalty too.
I feel like this is more of a discussion on balance than a bug issue, so might want to move it to discussion. But like TriRem said, since you get the villagers after you build the TC, you don’t really lose anything, since you essentially can get them at the same time your enemy has their TC up as well. At a balance standpoint, Mayans and Chinese are two top tier civs, so even if its not a perfect solution, its not like there’s plenty of maps that you can play those civs on.