In my proposal, after explaining the research question I had in mind, methodology part only suggests that I will follow a comparative approach and conduct surveys, I cannot understand why would an experienced supervisor would say those are not in his area. Or do you think it means he simply does not want to work with me? Should I reply and suggest I can change it? (which is something I really do not want to)

Have you asked your supervisor to suggest another methodology? If your supervisor really support you, there is nothing wrong in following his suggestion and make modification.

I haven't replied that email yet, he is not my supervisor yet I am contacting potential supervisors from different universities for the next year. It would be nice to work with him but at the same time he directly said my methodologies are not in his area so he can't be my supervisor, so I am not sure if I should insist, and how I should say it.

If you look at his past papers do they normally follow a quantitative or qualitative methodology and how do these relate to your proposed methodology? Although if he did not specify why he did not think your methodological approach was suitable for him. I would suggest he is not that interested in the project. As normally if they are interested they will try and persuade you to change your methodology to what they normally use. As most supervisors think their methodology is best.