As far as I can tell, the Base URL field seems to be ignored when a test suite is started. I initially set it to https://www.example.com and my first test case started with an open command of /index.html; all tests ran in the base url domain.
I then wanted to test in a subdirectory so changed the Base URL to http://www.example.com/test. When I started the test suite again, everything ran in the original domain not /test.
My workaround is to have the active browser tab open to wherever I want to test so not a show stopper but shouldn;t the base url handle this?