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qtractor, as many other jack clients, makes use of the auto-start feature of the jackd server.

if you're not using jackdbus, the auto-start command line is given by the literal contents of the ~/.jackdrc file (located at your home directory).

qjackctl, has this option to (over)write that precise file with the parameter settings it's using to start jackd itself, so that qtractor (or any other jack client) auto-starts the jackd server with very same settings.

hth.
cheers

ps. you can have qjackctl to be the one that gets auto-started in place of jackd directly, if you follow my instructions from here.