I don't want to put too much in the config files, so uncommon configuration options should probably still require changing lightsaber.ino.
Of the changes you listed, I think the WIZ820SD definitely falls into that category.
As for the sd card change, I've been considering ways to add some ways to override the pin map in the config file, so that you could change things in the pin map *if you want to*. Using ifdefs for every possible pin map is probably going to make the code really hard to read. However, until I've figure out the right way to do that, ENABLE_BUILTIN_SDCARD might be an ok solution. Maybe the simplest option would be to just move the pin map to the config file...