The command that you used to execute a test is using the default project settings and probably the script was executed against IE as a default browser for the machine.
To be able to modify the browser and/or other settings you can use a settings file for each different run. Please, see all arguments you can use in a ArtOfTest.Runner.exe command and scroll through the article to find an example for the settings file in jSON format.
I hope this will be helpful for you. However, if you need any further assistance, please, let me know.
Thank you very much for your cooperation.