I've done it both ways, many times.
I even cerakoted some machine tool parts with cerakote that was getting really old, and engraved after the cerakote.
Here's a lathe control panel I made that way in Cerakote cobalt:
Here is the one on my mill:
And a pulley speed range data plate, in cobalt:
This is a magnetic base mount plate on my lathe. Cerakote cobalt, engraved after the fact.
If you engrave before cerakote, you get a subdued look. If you engrave after, the markings stand out alot.
So, based on my experience, it works great either way and i've done alot of cerakoting.
Some of the engraving was done with a non-rotating diamond drag tool, some with a .028" ball mill @ 5000rpm.
On barrels, suppressors and receivers I engrave before cerakoting. I like the markings to be subdued unless the customer requests otherwise.
I made a run of 2" ball shaped automotive gear shift knobs a while back that I cerakoted, then engraved after. Unfortunately I didn't take any pics, but engraving circular text and a logo on the face of a sphere was fun.