Maybe, but stainless may not be the best material for that, because the oxide layer formed is largely chromia, and chromia is a motherfucker, which is why stainless doesn't rust. Etching chromium off the chromia sounds practically difficult but probably feasible; etching chromia while leaving metals sounds hard. Maybe molten sodium hydroxide?
Instead, you could choose a different metal whose oxides are easy to etch. Magnesium is probably the extreme case here, with an oxide that instantly vanishes in the weakest of acids, but if someone gave me a US$7000 fiber laser, I would try to keep the laser beam away from thin pieces of magnesium. But mild steel, for example, forms oxides that etch pretty easily with acids. I think copper oxides also etch easily with either acids or bases, too, and the copper itself is more resistant to etching.
Really, though, if you're molding silicone or chocolate, you don't need the high strength, flexibility, conductivity, etc., of metals. Maybe etch your grating into a material chosen for other properties. Glass, for example, is perfectly isotropic and has no grain structure to introduce into your cuts, and it has a low TCE. It sticks to silicone, but not to chocolate. Fused quartz is a glass with a near-zero TCE. I assume but don't know that the MOPA laser can ablate the glass surface.
Other amorphous solids might be more amenable to easy laser shaping and not stick to silicone. Sugar glass, for example.
Speaking of unreasonably dangerous things, though, it occurs to me that, if you laser-marked metal that was submerged in perchloroethylene (or carbon tet), the oxidation you'd get would be metal chlorides rather than metal oxides, and for almost all metals the chloride is easily etched with just plain water. You probably don't want to try that with aluminum.
Are you worried that the glass might overheat and break, or that it might produce a more dangerous specular reflection than Krasnow's polished stainless foil?
I think the reflections from glass will be about 5% of the reflections from polished stainless steel. So, while in general I strongly endorse your point, I don't think it applies in this context.
Is there any risk of the laser going through the glass and damaging parts of the machine? Or things such as refraction?
As I understand, those machines have a sheet of materials they can work with. This is probably the safest way to go: just stick with the materials the laser is made to safely operate on.
