In any program, you still have to execute a challenge somewhere. No program will issue certificates without that. In the case of certbot, you can simply write a small post hook that will transfer the certificates to cloudflare.

I would recommend reconsidering how you obtain LE certs. I ended up on Certbot too because it lets you own what is a critical part of your selfhosted identity. Plus Certbot works well and it's maintained by the EFF who also see it as a critical project. As a local script (basically) sky's the limit regarding automation.

This is personal preference but I strongly prefer to locally control critical automations about my setup (certs, DDNS etc.)

The certs produced by Certbot are portable and you can use them with CF, local reverse proxies, or whatever other infrastructure you may need. Just need to get a copy to the proper place (securely).

I guess in the bigger scheme of things the question is whether you're ok being tied to a particular service (like CF). I don't, and I also don't want to depend on the LE implementation of any particular reverse proxy (or their plugins).

PS: Oh and another tip: if you do end up using a CLI tool for certs, stick to Certbot. I've tried pretty much everything else and they all suck. It's actually unbelievable how much they suck. Arcane and opaque, the lot of them, which is not something you want from a critical tool.

Does cloud flare not do that?

They get certs so must have a way to get any kind of cert

Why not handle certs on your end and just use CF for proxy? I use NPM for cert automation with CF proxying. It's honestly ridiculous easy and I've had no issues.