I see these possibilities:
#1 Multiple file transfers that transfer multiple endings (*.csv, *.txt, *.dat ...)
#2 Copy/move all files that must be transferred into separate directory ("outgoing" using a JOBS object), then transfer files (*) from that outgoing directory.
#3 V12+: create EXEC VARA that identifies files to send and transfer each file seperately using a FE workflow
#3.1: <V12: SCRI object processing filelistvara / PREP_PROCESS_FILENAME on source system, for files that must be considered use ACTIVATE_UC_OBJECT to dynamically transfer file-by-file
I personally would recommend#2as it's most transparent and uses least job executions to do it's job.