Can I validate Let's Encrypt certificate on my origin if my site runs on section.io?

Yes you can.
We do not support Let’s Encrypt HTTP validation at the moment, but DNS validation will work fine. So if you are using DNS, that will still work.

section.io also uses LetEncrypt certificates and provision/renwal free of charge for any domain on our platform. So your site will still have a valid certificate if served through section.io. Additionally, our platform can be configured to ignore certificate errors on the origin. That way browsers connect to the site and are served a valid certificate from section.io platform, and then we negotiate SSL with your origin which can have a valid certificate or not.