If that were the case, iPads with cellular would be ineligible engraving. Besides, carriers are in the game for the service revenue. The devices aren't money makers for anyone except Apple.
The fact that Apple charges $0 for engraving and asks $45 for a silicone iPhone case tells me engraving is clearly a front end marketing tactic intended to reduce returns and drive gift sales. Apple could easily charge $20 for engraving if they felt it had no effect on sales or slowed manufacturing.