It could be that the phone correct determined the orientation but a pin was dirty/broken so it couldn't be used. When flipping the cable around the pin in use changes to one that isn't dirty/broken and so it works fine. USB-C may have a ton of pins but that doesn't mean all of them are needed to charge so flipping it can move a broken pin into the unused pins.
If we were still limited to domain specific connectors (one for storage, one for networking, one for audio, one for video, one for each type of user input) we'd still run into the same (non)issues: unless every revision of, say, displayport came with it's own unique connector, without digging a little deeper (checking some version/capability symbols) you don't know wether a given cable supports the latest feature set or not. The universal in USB is not the problem.
But (2) seems very unlikely. Most consumers just won't even consider that it has an orientation, and after it fails a few times chuck it in the bin or send it back. If it comes with a device (i.e. printer or monitor comes with a non-reversible cable) they're likely to send the whole device back. That would be a ridiculous false economy for the manufacturer.