Doing anything build-script related in Jenkins, whether Pipeline or freestyle jobs, is definitely an anti-pattern. All build-related scripts should definitely be in standalone scripts / build tool config files (make or whatnot), for reasons you describe.
Jenkins should be there to handle the "side effects", as I view them. In our case that's stuff like integration with git PRs (posting results of linting, building, unit tests), sending emails when new builds are available, integration with JIRA (we automate some workflows), publishing artifacts to an internal server, etc.
Conversely, putting any of those side-effects or stateful steps inside build scripts is a bad idea, and it leads to not being able to run build scripts locally without worry of messing up a JIRA workflow or spamming people with build emails. Thus, they should be stored only in Jenkins.
These are all mistakes of my predecessors that I am still living with to this day.