Eventually the goal is to have all sorts of color tools in the application. Per object color tint, global color palettes, etc. For now working in grayscale solves a lot of problems on my end. Sorry that it's a hassle to get the output to a specific palette at this point. I've gotten good results with blending color overlays on the output, but if you have a specific palette there will still be a lot of work in color replacing.
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Thanks for the explanation. I found a YouTube video and even something on Twitter that demonstrated actual use. I'll keep a lookout for more videos like that as I feel I'm missing something. Are there plans for tiles other than for buildings/machines? I suspect with the right parts you could make Chibi looking characters/monsters.