This could be possible but you would need to use some scripts to perform this.
Ideally Acrobat would perform comparison in a full fledged way.It would not filter content except you could compare specific pages of two documents or simply compare texts or pictures.
Please have a look at the compare documents option to get more clarity.
Sorry for the problem you're facing. You can filter the results of the Compare Result file in Acrobat XI using Filter Comments option as follows:
- At the top right in Acrobat, click the Comment pane.
- Under Comments List Panel, choose Reviewer as Compare: Delete in Filter comments menu.
Please reach out to us in case, you face any issues. You may also log a Bug Report or make a Feature Request at: Adobe Acrobat - Feature Request/Bug Report Form
Also, we have significantly improved Compare functionality in our new release of Adobe Acrobat DC. Please update to the latest version to give it a try. The new Compare Files Tool offers a Side-by-Side view which provides a better experience in identifying differences and a modern UI.
Latest version for Adobe Acrobat DC build number: 2015.020.20039 (Continuous).
For more info about the new Compare tool, visit: https://helpx.adobe.com/acrobat/using/compare-documents.html as well.
If you are still on Acrobat X or XI, you can check out our trial version at: https://acrobat.adobe.com/in/en/free-trial-download.html
Adobe Acrobat DC Team.