I don't know it this is a recommended way, you can get a better answer in the CCS forum, but what works for me is to edit makefile.defs, which is located in the top project directory, and to add:
./configPkg/linker.cmd: ../table.txt
assuming table.txt is also located in the top project directory. The file linker.cmd is one of the files generated from the CFG script, so this dependency will force evaluation of the CFG script.