What you are describing is a standard way of making router table tops. More commonly, though, both sheets would be MDF, and they would be laminated to reduce friction and protect the wood from absorbing moisture.
I have tried twice to get a perfectly flat top this way, and I have failed. I am not saying it's not possible, but it is difficult. Living in North Carolina, the humidity changes are substantial; perhaps it's that in my case, or it's just my lack of skills. In the end, I did also get a Rockler table (just to get it over with), and I am dealing with the same issues you are describing. I also mounted a frame underneath. It's still not perfect, but I think I can live with it.
If you look around, you'll find that many people are struggling with getting their plates absolutely flush. There are plates that are cupped by design. All this tells me that one can live with such tolerances - in most cases.
If you really want to get a flat table you'll probably have to look at some material other than wood. Phenolic or cast iron come to mind. Humidity won't affect those. Other than that, a mounting plate that's as small as possible might be an option. There are circular plates available that are just slightly larger than the normal base plates routers com with. You could give that a try, but you'll still have to start out with a flat table top.
Good luck! MM