I like Cloudflare as a company but I’d be weary about paying for my domains and hosting my DNS with the same publicly traded company with a severe lack of public customer service outside devs getting mad on twitter (guilty!).

If cloudflare gets mad at you (even accidentally) and cancels your account then you lose everything. At least if you separate them, there is a chance that you won’t lose access to both at one time. Given that domains are generally a one time setup after purchase (especially if you use cloudflare for DNS) then I think the minor inconvenience is worth it, personally.