Let me, please, step in this discussion as Plamen is out of the office.
I reviewed the conversation so far and it seems like you have sorted out your doubts - the Test Studio CLI runner can only use its specific options, which will affect the particular run, but not the application under test.
So, having that said, you can try adjusting the helper class file in a way to be able to pass the necessary variables and parameters to each test.
The idea you have about modifying the settings file doesn't seem to be an option, because it cannot be accessed from within the test. Also setting any data in it, which is not expected, may cause the CLI runner to not accept it as a valid settings file.
I hope the information shared so far is beneficial for you. Of course, in case you have any other questions, please, do not hesitate to get back to us. Thank you once again for your cooperation in this discussion.