On the left is another phyllotaxis render (using Mathematica to explore fractals that model flower structure). To paint in multiple colors, I rendered to an SVG with multiple colors (3) and:
- apply masking to tile, transfer tape in this case
- Do first color engrave, ignoring other colors, at full power / 700 speed.
- paint
- Do second color engrave ignoring others, etc, (carefully)
- paint
- … repeat as necessary …
The key was to stick some magnets to the honeycomb so I could easily remove the tile and then stick it back in to maintain the alignment between cutting passes. From there, required minimal cleanup of any paint that bled underneath the transfer tape.
It also has a transparent coating on it that should be pretty durable. Specifically, I grabbed Mod Podge’s dishwasher safe sealant, thinned it slightly with water, and then poured it on. Unfortunately, I introduced bubbles when mixing and didn’t let them settle out due to impatience. Still, looks pretty darned good. 
For the moon:
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paint a tile black (or whatever color) with water based acrylic paint (Michael’s has assortment packs of 12 colors for $7 in our neck of the woods). Might want two coats.
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grab a photo, preferably black and white
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invert photo
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engrave; this was full power @ 850 speed. I used “vary power” which worked well at achieving a gradient on the relatively thick coat of paint I used. If you have a thin coat of much more evenly applied paint (working on that part), then I suspect pattern or random dots may work better.