As an aside this is not quite right. The process through which it is sintered actually does erode into the surface and depending on the material and settings can be quite notably recessed even with the film leftover.
Here’s the best photo I could get from my phone using my inspection magnifier on a stainless tumbler I have lying around. The raised lip of the bare stainless is there; you can even catch your fingernail on it. This isn’t even the deepest I’ve run.
As for the OP’s question, I think engraving the top of the jars is fine but they’d need to be sterilized even if you covered the inside section because none of our equipment is clean enough for food stuffs.
An autoclave might solve that problem but I’m unsure how BPA handles it. There may be a more adequate procedure.
Additionally one doesn’t have to spray the moly, it can be applied with a paste in a thin layer.
I’ve done plenty of food stuffs with the process but they’ve all been things I can adequately wash and seal out the insides during the process.