I usually like printing on both sides of a piece of paper.  For arcane
reasons, this is called "duplexing" (a lot of printing terminology is
arcane).  When I buy a printer, I always try for one that can do
automatic duplexing.

Context: I use Fedora with Gnome and CUPS.

For years now, I've been a little perplexed why my printing from GUI 
applications is duplex and from other applications, is single-sided.
I now know more of the answer.

From the GUI settings menu, you can set default printer options.  From
the print dialogue box of GUI applications, you can also set this
option.

        Page Setup: Two-sided can be
                One Sided
                Long Edge (Standard)
                Short Edge (flip)

These options don't affect printing from non-GUI programs (eg. lpr and
alpine).  For that, you use the lpoption command
        lpoptions -o sides=two-sided-long-edge
(Notice the different terminology?)

It surprised me to learn that options settings are persistent.
lpoptions(1) saves the setting in ~/.cups/lpoptions.  Reading the
lpoptions manual, I thought that it was the other way around: that a
user could edit this file and lpoptions(1) would take that as a
starting point.  A good thing too, since the format of the file is not
documented.

You can also put the options on some commands directly, for example
lpr(1).

If root executes lpoption(1), the file /etc/cups/lpoption will record
the result.  Ordinary programs that are not running as root consult
this file as well as ~/.cups/lpoptions

It seems goofy and annoying that the two different ways of
setting printer options don't communicate.

Printer settings can get even more complicated when you look at ppds.
I think that is because different printers have different settings.
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