Although both merging and joining processes involve merging of Outlook PST data files into one consolidated file, but there is a huge variation between them. With merging Option save users saves time to handle numerous PST files and reduce backups and other management overhead.
Whereas, Joining PST files generate a consolidated PST having all the email items irrespective of duplicate PST items. All joined PST files will preserve in a separate folder inside big joined PST file. All data items like email, calendars, folder, task, contacts, etc. remain intact.
But Merge operation involves some smart process as it will generate a big single Outlook PST file and all the folders of selected PST files share same root folder and respective of hierarchy like it was in original individual PST file. After merging process, all same name and hierarchical levels get merged and generate a large complete folders structure of all PST file. The best feature of this option is that Duplicate email items like contacts, emails, and other data gets discarded and you will a get a much better and compact PST then the individual PST files.