Unfortunately the "Enable Commenting in Adobe Reader" function of the Adobe Acrobat Pro software is not a feature that we can support with our software or that any other third party vendor can support.
While we would love to support it this feature is not part of the official ISO PDF specification and it's Adobe's attempt to use their monopoly with the free Adobe Reader and screw the rest of the PDF world. Where the remainder of the security features like allowing printing or modifying the document are basically a setting in the format the "Enable Commenting in Adobe Reader" is controlled by Adobe by the use of a private key to generate the required digital certificate value for each PDF.
We have tried in the past to automate Adobe Acrobat Pro to enable this value if you also have Adobe Acrobat Pro installed but that also has been unsuccessful. It appears that Adobe does all they can to prevent it so you would have to buy their Lifecycle Designer to batch enable PDF files for the "Enable for Commenting in Adobe Reader" feature.
We suggest you tell your clients to use our AcroPlot Matrix or one of the other third party PDF Viewer and Markup tools instead of relying on the Adobe Reader.