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doesn't "auto-connect" tell you something while on the bus proprieties dialog (View/Buses...) ?

if you really don't like the default behavior (Master buses auto-connected to system:capture/playback ports for instance), please consider a new session template which is a session file like any other one but with no media content; setup there any input/ouput buses and tracks as you like, then save and make it the one to show up everytime qtractor starts a new session from scratch (eg. File/New), by making it a "New session template" (cf. View/Options.../Display/Session).

hth.
cheers