when building from the command line, the settings set in the IDE are not used. To pass them, you can add them to build_project.sh with the -c option. For instance, if you wnat to pass -p 4096 to set the blocksize to 4096 and -I10 to set the input gain to 10dB, you do:
build_project.sh -c "-p 4096 -I10" ./
To see all the command line options passed from the IDE to the program, get on the board and run make -C ~/Bela ideconnect, this will display the IDE's console output. With that open, run the program from the IDE: the actual command line options passed to the program will be printed in the terminal session.