When you run OmegaT from the command line, you can specify the path to a use configuration folder that is not the default one, e.g.
java -jar /path/to/OmegaT.jar --config-dir=/path/to/config-dir
If you're running OmegaT from a launcher, you must add argument to the command your launcher uses.
If you're running OmegaT from user, you must do:
./gradlew run --args="--config-dir=/path/to/config-dir"