Hello,
I also agree with the idea to abolish the .pd* config files in homedirectory.
Instead there should be a default settings patch, i.e. ~/.pd-settings.pd or ~/.pd/init.pd or something of that nature. Probably it's a good idea to use have ~/.pd/ to start with, so one could put gui pluggins there and other things. Though there should be a shortcut in the menu to edit open the init patch.
Earlier I have had an idea that the configs should be done in Tcl instead of the format that they have, but if one uses pd without gui, Tcl scrips cannot be interpreted.
The #purest idea would be to use patches for setting.
Ilya