When I did some casting, I did exactly that. I molded a line where the lip was to be cut. Molding a pip for the hardware is a good idea, ensuring that your baits are repeatable.
As for screw eyes, Mounting them in the mold will be difficult as they have no support. Would be much easier to mount a wire harness, as it will have at least three points of contact with the mold.
I preferred to drill the holes after casting. I do not think you can fit screw eyes as you would with wood, with a smaller hole then screw in. The cast material is very hard and a bit brittle, could cause problems with the threads breaking or even fracturing the body. I could be wrong on this.
I would prefer to drill a hole so that the screw was a sliding fit and fill the hole with epoxy or similar.
So that the epoxy plug cannot pull out, someone suggested widening the internal portion of the hole, forming a wedge, by angling the drill. Apart from the wedge, this will also rough up the internal surface, giving the epoxy more grip.
These are good questions and deserve a few more replies.
Dave