The kerf width of the laser cutting beam is pretty much the perfect margin for proper tolerance on fitment. So I approach the design process with zero allowance, knowing that that kerf width will be involved.
I used a mixture of oil based Minwax wood stain in some areas, and acrylic artist paints, which are water-based, in other areas. My plan is to seal everything in with polyurethane. As much as possible, I try to avoid putting the acrylic onto a place where an oil based stain has already been applied.
For some I did, but in most cases I painted after, even if I had painted before. My laser has a slight misalignment on its beam, and I get a little bit of smoke, soot, and scorching on areas that were not in the cut path, and it requires a little bit of sanding and clean up afterward. So in some cases I wound up sanding off the paint that had been put on before the laser. In that instance, the paint kind of acted like a sacrifice layer.