Not sure if there will be a separate app to edit the config file. The idea is to allow users to customize their local versions of TIC with the config file and TIC doesn't have access to edit config.lua from inside.
I'm going to add FONT (or TEXT) api function to render variety width font directly from the spritesheet, PRINT api func will be used to draw text with only system font. As for palette, you can define it when game starts by POKE or MEMCPY functions.