Whilst it varies by region, the cost of certs is often bundled with the cost of the associated manual. Typically, dive centers get an account 'credit', or paper application form, to process a PIC with each course manual they buy.
You have to sell a manual with each course... So it keeps that initial cost down. Standalone credits are less economical to purchase.
Maybe some shops are 'separating' the cost of manual and c-card fee? To give some impression of 'added value'??
Or perhaps some shops are adding a 'processing' surcharge to the cost of replacement cards.... if they're the ones ordering it for you.
Shops are, after all, permitted to resale PADI products (manuals, certifications etc) at whatever price they deem fit. It makes sense that this cost should cover staff processing time, shipping (manuals, certification processing envelops etc), and the need for capital to be invested in stock.