The Indeed listings are dynamically displayed on the JobRoller site rather than imported into the database, so I believe what you describe isn't an issue in this instance? We made changes to JobRoller some time ago to accomodate changes Indeed made which is outlined in
this blog post. Locally listed jobs are displayed with Indeed jobs listed either above or below the results as "Sponsored results" based on the keyword search terms used. Making changes to the search etc also as you describe would require customization on your part. Our themes are not encrypted, so you are free to make modifications as you wish. Currently job seekers can apply for jobs listed on the site using the "apply online" button, and if selecting an Indeed listing, they are already redirected to the Indeed site for further information/application options. Thanks.