According to the man page, command line options for xboard can be placed in ~/.Xresources.
This manual documents version master-20110822 of XBoard.
OPTIONS
This section documents the command-line options to XBoard. You can set
these options in two ways: by typing them on the shell command line you
use to start XBoard, or by setting them as X resources (typically in
your `.Xresources' file). Many of the options cannot be changed while
XBoard is running; others set the initial state of items that can be
changed with the Options menu.
Most of the options have both a long name and a short name. To turn a
boolean option on or off from the command line, either give its long
name followed by the value true or false (`-longOptionName true'), or
give just the short name to turn the option on (`-opt'), or the short
name preceded by `x' to turn the option off (`-xopt'). For options that
take strings or numbers as values, you can use the long or short option
names interchangeably.
Each option corresponds to an X resource with the same name, so if you
like, you can set options in your `.Xresources' file or in a file named
`XBoard' in your home directory. For options that have two names, the
longer one is the name of the corresponding X resource; the short name
is not recognized. To turn a boolean option on or off as an X
resource, give its long name followed by the value true or false
(`XBoard*longOptionName: true').
I see that this is no longer the case, and that /usr/local/etc/xboard.conf and ~/.xboardrc now store preferences.
So the man page needs to be revised.