I don't think that you're missing anything. On macOS there is no option through System Preferences to define printing defaults. Most people are expected to use presets and accept that as sufficient. With more and more apps providing their own print dialog (ie: Google Chrome) that renders presets less useful, or at least more annoying to use as you have to invoke another window before printing.
To set printing defaults you'll need to access the Common Unix Printing System (CUPS) configuration page. Open a browser and enter localhost:631 to bring up the cups page. On most versions of macOS that is disabled by default. If the CUPS page doesn't load it will show you the command to enter in terminal to enable it. Once you've entered the pre-requisite terminal command go back to the browser and refresh the page.
Once you're in CUPS select...
Administration->Manage Printers
Click on the name of the printer that you want to edit the defaults for
Click the dropdown menu that says Administration and select Set Default Options from the dropdown
Modify the settings that you want to modify and at the bottom of the screen click Set Defaults
