Customized Linting mismatch with Schema linting

Description of the bug

I have a customized internal pipeline that uses the nf-core template but uses only portions of it (as introduced with 2.5X release of tools):

My .nf-core.yml (only the relevant parts of it):

repository_type: pipeline
lint:
  nextflow_config:
  - manifest.name
  - manifest.homePage
  - params.input

This results in linting saying config variable is ignored:

But nf-core lint says:

Which is true - it is neither in the schema nor in nextflow.config. If I remove the above linting exception, it throws a warning that the pipeline is missing --input.

Cross checking by just running nf-core schema lint . says "all fine":

My expectation would be that the linting warning should not even be there....

Command used and terminal output

nf-core lint / nf-core schema lint

System information

tools 2.6, linux on centos 7