The Jenkins git plugin can't combine the contents of two different repositories into the same root workspace folder. Thus, you can't use the Jenkins git plugin to have a single job workspace root folder which contains both CORE and SITE repositories at its root.
You can (with the pipeline plugin, or with the multiple SCM's plugin) checkout multiple repositories into subdirectories of the workspace root folder. You could then run a build step which combines the contents of the "WP-CONTENT" directory from each of those subdirectories into a single subdirectory of your choosing inside the workspace.
I'm not sure what you mean when you say "Both the folder will get merged while deploying the code thru GIT".
Thanks,
Mark Waite