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OP's security concern is valid. Different CAs may differ in the challenges used to verify you to be the domain owner. Using something that you could crack may lead to an attacker's public key being certified instead.
This could for example be the case with HTTPS verification (place a file with a specific content accessible through your URL) if the website has lacking input sanitization and/or creates files with the user's input at an unfortunate location that collides with the challenge.
This attack vector might be far-fetched, but there can certainly be differences between different signing authorities.
But even if you use GoMommy extra super duper triple snake oil security checked ssl cert, if I trick LetsEncrypt to sign a key for that domain I still have a valid cert for your site.
You're right, my bad.
Certificate pinning?
Also all let's encrypt certs are public. So if someone malicious gets a cert for your domain, you can notice.
(Thats also why it may be a bad idea to use that for secretButPublicStuff.Yourdomain.com certificate transparency logs are a great way to find attack surface.)
edit oh certificate pinning has been deprecated in favor of checking transparency logs.