With the SMARTDAC+ GX/GP series' main unit FTP server function, can I acquire recorded data files on the main unit CF card or internal memory from a PC on a local area network?

Yes, with the FTP server function. See section 3.3, "Accessing the Measurement Data File on the GX/GP from a PC (FTP Server Function)" in the user's manual.
User's Manual (IM 04L51B01-01EN)