What POS integration buys you
Accuracy. The reward is attached to a real transaction, so a rule like "one stamp per $200 spent" is enforced by the system rather than by staff remembering it. Refunds can claw stamps back. Nobody can be stamped for walking in.
That is genuinely better, and it costs a POS subscription, its hardware, and being locked to one vendor.
What QR gives up
The system records a visit, not a basket. It cannot see what was bought, so any spend-based rule depends entirely on staff applying it correctly.
It also cannot claw back a stamp when an order is refunded, and it will stamp a customer who bought the cheapest item on the menu exactly as generously as one who bought the most expensive. For a café where tickets cluster, that hardly matters. For a shop with a wide basket range, it does.
Which to pick
If you already run Square and your customers pay by card, Square Loyalty is the better system and the $45 is buying real accuracy.
If you take cash and transfers as often as cards — the normal case for a small business in most of the world — a QR platform running from the phone in your pocket does the job for a fraction of the cost and setup.