Can we use ProcessBatchData method of SPWeb to apply unique permission on a list item? I know this method supports insert/update/delete but I am not sure if we can apply permissions in bulk.
I think you may have look into the below third party tool :
Item Permission Batch
Bulk assign, remove or change SharePoint permissions
for multiple list items or documents.
This tool has free as well as paid version - if this is your one time use, you can download it and make use of this.
The above tool can be downloaded from here.