It has worked with glass bottles in Sweden for I know many decades, maybe a century, unsure. Unfortunately glass bottle usage is down and plastic usage is up.

The German mineral water industry started using a standardized glass bottle in 1969, all of these are reused: https://de.wikipedia.org/wiki/Normbrunnenflasche

If we could do it 50 years ago, we can do it now. It's a solved problem.

You don't have to make the system perfect. You have to make it cautious. At any time it suspects a bottle may be too dirty or not getting cleaned for some reason, it should reroute it to manual inspection line and/or straight to remelting. So now you lose 30% of your yield, but the rest is clean and sterile. That's a good starting state, from which then you can optimize the contaminant detection.