You can see this on the post composer page when using the emoji picker. When custom emojis are loaded, they use S3 endpoints directly, like:
https://cdck-file-uploads-global.s3.dualstack.us-west-2.amazonaws.com/meta/original/3X/1/d/1de8f76096f76cf393640bdcff387ec9ae33dd3e.gif
This shows the paths aren’t being converted to CDN URLs as expected.