I think I'm going to junk this whole read from config.ini strategy in favor of command-line arguments real soon. This just isn't worth it... Would anyone have a problem passing in arguments instead of editing the config.ini?

Fine with me.

Well, I think the config.ini solution would be better. It just is the established place for configuring the empeg. And it is easily available via (j)emplode from almost any computer (because you can edit it via either serial, USB or ethernet), while any other place would only be available via either serial or Ethernet (with HiJack and/or telnetd installed).
I really think that any third party software that isn't storing all of its configuration in flash (and is fully configurable on the player itself) should store (additional) configuration options in config.ini.

cu,
sven