As the replies already indicated there are ways to do the job. Which ever method you choose you are going to run into a few additional problems.
The first of which is that just adding a coat of tinted poly to the light area will leave you a demarcation line, sort of a self induced witness line, between the color coat and the existing coats. That line is going to have to be feathered in and that is going to compound the problem of matching the darker part of the project. The next situation you could run into is that should, somewhere down the line, this color coat, being a top coat, get damaged, repairing it will be difficult because not only will the color coat be damaged but there will be no way to repair the damage without affecting the color coat.
There are other ways to address the problem but, for simplicity's sake I'd suggest you apply you color coat up to the point needed then continue to apply clear varnish to the rest of the project. I'd also suggest a fourth top clear coat over the whole thing to protect that color coat without leaving any demarcation lines.
Too bad the situation wasn't reversed with the darker wood on the bottom and the lighter on the top. Most times you can get away with that sort of thing because it still looks balanced. Having the darker wood on the top sort of makes things look unbalanced and top heavy.
As an aside, I'd use an oil based aniline dye to do the blending rather then a stain or pigments/artist colors.
Just a thought