I wouldn't like to test this on a keeper part but you could try running the anodized part as you normally would and then hitting it again with Cermark. I would not move the part between runs but mask the interior of the machine and spray the Cermark directly on the part or spray it into a cup and brush it on. If you have a current Epilog, I think you have the encoder strips which you need to keep free of Cermark. My machine is nearing 10 years old and does not have the strips. I have sprayed Cermark on a few parts while they where in the machine but I don't make a habit of it since it's probably very abrasive and if there is any on a lens or mirror it could destroy it.
The Thermark LMM6046 looks like it would work but based on Thermark's notes, it may have a bit of a learning curve.
Another option would be to mask the part and vector cut the text. Then you could powder coat the parts and bake them in a cheap toaster oven.http://www.eastwood.com/hotcoat-powder-coating.htmlhttp://www.harborfreight.com/catalogsea ... t?q=powder
I've never used a powder coating system before and don't really know if it would work but I think it would.