This is similar to the customized docker image that we build for Jenkins.
We just leave the $JENKINS_HOME/jobs folder intentionally inside the container. so that all job configurations are part of the docker image.
A Jenkins instance started from such an image has all its jobs available out-of-the-box.
There is in fact no option to tell Jenkins to use a different jobs folder other then $JENKINS_HOME/jobs.
As a workaround you could replace the $JENKINS_HOME/jobs folder by a link to e.g. /var/jenkins/jobs and let docker map a volume to /var/jenkins.