When you do a patron import you can set the values for everything except the messaging preferences. The CSV should have a field for that and the form on the page should also offer the option of setting a blanket default for what's being imported. It's my understanding that this ability is there in the command line script, just not the GUI.
*** Bug 3231 has been marked as a duplicate of this bug. ***
This is still desired and came up in training today.
Currently the import script will use the defaults from the patron category of the imported patron.