Now that we know the answer, is it easier to reason our way to a correct explanation?
Yes, of course! Well, maybe not the correct explanation. Hindsight devalues science.
Just like with the Feynman Sprinkler, I was able to convince myself in advance of two contradictory outcomes. This shows that I don't understand the mechanism either. We need more data!
From Boy Scouts I recall the fire triangle showing that the candle needs heat, oxygen and fuel to continue burning. From everyday experience we see that burning candles provide their own heat and do not usually go out in the absence of strong wind. The photo shows that the fuel supply was not used up. So I feel confident (consistent with our predictions) that oxygen starvation was the cause, either because oxygen was used up or carbon dioxide displaced the oxygen.
We could try attaching some threads, spiderwebs, foil strips, dandelion seeds or something similar to the inside of the glass next time and see if we can detect air movement in the upper, middle and lower sections. We could pay attention to any smoke that appears after the candle goes out, to see if it follows any established pattern of air flow. We could try experimenting with a cardboard tube to make a chimney which would draw fresh air up from the bottom and see if we can put the lower candle out first.
To test for carbon dioxide, we could try using a sensor. It would be interesting to see how the values change at different heights.
Thanks for the quiz!