What are some key considerations to generate QR codes that are compatible with stores' POS systems? Is this relatively complicated for an MVP?

QRs are simple links, typically URLs. To perform any kind of interaction with a 3rd-party system, you need to understand what parameters this system can take as part of a URL and see if it performs the expected use case well. My suggestion is that if you can generate the right use case by typing a URL in a browser, you can also support the same use case via a QR. The QR is not where the challenge is. I hope it helps

I've deployed QR systems around the world, and created MVPs for retail systems.
Most POS systems are set to scan traditional 1D barcodes. It is likely that whatever solution you come up with, the POS will need to be upgraded.
A QR code can hold up to around 4,000 ASCII characters (it's a bit more complicated than that) - so the code can contain a database ID, URL, contact information - anything you like really.
The complicated bit is what you actually do with the data once scanned. Is it for a loyalty card? Payment? Stock keeping?

QR codes are not typically compatible with POS systems, as POS systems scan bar codes (typically UPC codes). Perhaps you can program POS systems to scan QR codes, but having been a retail buyer at Target, there is no incentive for retailers to link QR codes to POS systems. Can you elaborate more on what you're trying to accomplish?