Last time I used Cloudflare I think their settings default to only "Origin SSL/TLS" (or whatever they call it), which wouldn't encrypt anything between Cloudflare and the origin, it would only encrypt data between Cloudflare and the end-user/browser.
TLS doesn’t matter for End-to-end encrypted stuff though, you could exchange the data over Telnet and it would still be secure. The content itself is already encrypted before being transmitted and can only be decrypted by the receiver.
But the Signal client encrypts images before sending them to the Signal server. If it padded out the images at that point, the images would all be indistinguishable from each other unless Cloudflare were actually able to break the encryption (which would completely undermine the entire security model).