When looking at the basic technical differences between REF and CPT files there is not a lot of system differences. Both of them create physical files and both have logical files.
The difference for the 2E model is in how you generally use these two types of files.
The REF files will primarily be used for master data. This could include something like a zip code file with names of stores or other files that you use. It refers to relationships when you want to have an editable list of values for a prompted field. The REF file type will automatically create a SELRCD (Select Record) and an EDTFIL (Edit File) as well as the CRTOBJ (Create Object), CHGOBJ (Change Object) and DLTOBJ (Delete Object).
The CPT file is primarily used for transactional data. An accounting system is a great example of this. New records are added on a regular basis. Capturing these detail records or transactions provide the primary difference about the CPT file vs. the REF file. Also, the CPT file will only automatically create the CRTOBJ, CHGOBJ and DLTOBJ.