Well OSX is actually very Usr and Permissions specific, but unlike linux distro's there is much more leeway in giving access to files for other users. Things in the /Applications/ folder, for instance, are suppose to read and write accessible to everyone. The home folder is very much accessible only by the usr. Unix specific folders (etc, opt, local...) also exist but are hidden from the average user.
Actually now that you mention it, some of the files generated by the package aren't even read accessible for users other than the person who installed the package, specifically the /usr/local/etc/xboard.conf. Or really the /etc/ folder before it. I need to fix that. Don't worry in OSX permissions are a pain as well.
As for the .../etc/xboard.config file should say how about this?
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I know you wanted the wood textures to be default, and were always accessible in the .xboardrc
-soundProgram is a must as it is OS specific, but is also accessible.
And yes the user can/should put in -saveSettingsFile ~/xboard.ini if they really want to in the /App../xboard/xboard.conf.