I have a typical GitHub Org folder set up for Enterprise Cloud GitHub org with internal repository type, that is using GitHub App credentials, and the pipeline was running on a PR draft from a private fork. The very first step the pipeline is doing - readTrusted step, and I got the following:

05:16:37 Connecting to https://api.github.com using GitHub App for github.com/xxx
05:16:37 Jenkins-Imposed API Limiter: Current quota for Github API usage has 9 remaining (6 over budget). Next quota of 60 in 44 min. Sleeping until reset.
05:16:37 Jenkins is attempting to evenly distribute GitHub API requests. To configure a different rate limiting strategy, such as having Jenkins restrict GitHub API requests only when near or above the GitHub rate limit, go to "GitHub API usage" under "Configure System" in the Jenkins settings.

On the enterprise org GitHub App credentials are having hourly rate limit of 15k requests. 60 is what usually is given to anonymous user. As the repo is internal and the fork is private - it would not have had access with anonymous user. I am puzzled as to why it was thinking the quota was 60/hr as like it was anonymous while in fact it wasn't.