I discovered a relatively simple solution to this problem: Just open any file with an application that allows such customization (Word, Acrobat Pro, etc.), customize the print settings as desired, and then cancel printing.
Now you can go back to the troublesome application and choose Last Used Settings from the Presets pop-up menu, and the system will use the more-complete settings from the other application.
[crarko adds: I haven't tested this one, as most of the apps I use have the full print dialog available.]

