This is certainly possible via an Event script. The Custom Target Application will by default output the file contents in a predefined order (Account, Entity, UD1,UD2,..UD20, AMOUNT). However, you can put some file parsing code in the AftExportToDat event script to reformat the file output to your meet particular requirement.
Since event script is not supported in PBCS FDMEE, do I have another option to reach this objective?
Ok, with PBCS you are obviously more restricted so the simple answer is no unless someone out there knows of some undocumented FDMEE feature in the cloud. You will need to look for another option such as
I guess Hybrid mode is planned for PSU100.
With that you would be able to use on-premise FDMEE 184.108.40.206.100 to extract data from PBCS and load to custom application file.
As you would be using on-premise FDMEE you can use event scripts.