Indeed, it’s not really easy for now with Fontself Maker to work on a 3-layer font and get adjusted spacing and kerning between layers. I think you may have 2 options to consider:
1/ Turn your 3-layer font into a family of color fonts with your different color variations. Ok, ok, you have to create the different colored vesions and import them . BUT: if you name your objects, you make your glyphs import easier. And once you have spaced & kerned one font, you can import & apply theses metrics to the others.
2/ Switch to Glyphs app. It seems to be doable but not so simple: https://glyphsapp.com/tutorials/creating-a-layered-color-font
Hope it helps.