Alignment across all elements of the concept paper is important because it shows that you have a clear grip on your project and that your thinking is orderly and logical.
In a concept paper, you are essentially laying out the "why" and the "how" of your research project. If you have understood your project properly, the "why" and the "how" will be aligned. You will be able to clearly state the research question and to situate it in the literature of the field. You will be able to say why it is important. Then, very importantly, you will be able to lay out a research design that is truly aimed at answering the research question that you have proposed.
If you cannot align these main parts of your concept paper, it will be clear that you do not have a coherent research project. You will not get your grant or you will not be able to go ahead with your thesis or dissertation.