It doesn't matter if it looks different. All that matters for your purposes is that it scans to the result you are looking for. If you want to know the reasons for why the code looks different, then you will have to explore the specification and do some technical work to decode the complete contents. It won't really give you anything but the satisfaction of knowing something new about a technology, but it also won't be a complete waste of time since you will learn something new.
As for the scanner reading it correctly, well you won't know that it will unless you know what specification(s) the scanner is capable of decoding. Just like 1-D barcodes, QR codes have many implementations and not all scanners are programmed to decode all of the possible types or encoding methods. You will need to take some valid examples of QR codes they can scan and analyze them to find out which specification they are using so you can produce codes matching that specification. That's the only way to be certain if you don't have access to the scanners being used. It takes work and knowledge, but if it's important to you, then that should not be an insurmountable hurdle.
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