I don't think it's a good idea for git-clone to do this job. It's unsafe and unreasonable to modify a local existing file or override the local config without the user's awareness or permission.

I don't know why you'd like to do so but I think you can do it through other means. For your team members, you could tell them the rules they must obey during the development. For a random user who may clone your project and contribute, you could write down the rules in README or project introduction. Users should be allowed to do whatever they'd like to in their local repositories. But when their commits are to be merged or applied into the blessed repository, you could set up barriers to those unsatisfactory commits.

For example, if you don't want files that contain dos style line endings, you could detect them in a pre-receive hook, prevent the push, and then respond in the error message to explain why the push has failed and suggest what to do to fix the error. Making a specific git-config can be included in the suggestion.