You do not need to replace the file, although you do have to place your new one in the same directory as the original, edit GraphicAssets.xml look for color_pick_rainbow and change it to your new png.
Coming from you (author of a perfect sample mod with many such custom Factions).. i can certainly refer to that exact process of manipulating whichever files. Not everyone has such skills (at least i'm just beginning to study GC3 assets) -- so, i simply thought Stardock devs would have been doing us a favor & follow through on their "promises" to enhance the XML schema potentials (as quoted).
They have kind of(vaugly) held up on their promise of a better modding solution by adding the Civilization Builder, where myself I do find this lacking, due to my knowledge (and its not all mine, its been gathered from all manner of users from these forums), I can substitute this with xml modding, I am also hopefull they will expand on the current civilization builder to atleast include system creation rather than the limited predifned selection we have now.
Currently, i think the Steam interactions with the usual ingame tools are lacking scope or direct methods that most inexperienced modders should have a hard time mastering. Thus why a more friendly set of editing toys would facilitate solid creative projects. I admire your cool results when it comes to packaging.. and fully expect having fun trying to understand how to reproduce such a success.
Yet -- Steam still can't really handle that kind of complexity directly at the moment. That's what i meant by referring to Cari's comment.
I would love to see workshop support for xml mods and some modding tools, I am not going to hold my breath though. Modding in general for this game is progressing on an upwards scale with each new content and free patches. More to do with getting my (our?) hands on new examples/different examples of existing code that stardock uses. Less trail and error for modders for functions/actions. Be nice if stardock commented ModifierEffectTypes.xsd and explained what function/action requires what paramerters.
I have always made my mods with Civ5's SDK (Modbuddy), you can even get Modbuddy to read the GC3 scheme files so any xml errors detected will be debuggable within the sdk. Its quite a fiddle to get the scheme files into the correct location within your solution directory (thats where it looks).
EDIT
I have not used the ingame builder to make a civilization, my Star Trek races were ported from xml civs. (Copy'd via the builder). I have used the Shipset builder, I do find this a bit clunkey to use, when you have 3000ish designs downloaded from the workshop its very much a mild anoyance scrolling through all the ships due to the limited search options.
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