Any question answered...

a tendency to hand-wave away extremely significant factors, and present opinion as fact

I'm not sure how significant tax/subsidy is in the question of whether price is a good proxy for the relative greenery of rail over air or vice versa. Obviously it's a factor, and in some circumstance it will be the factor which, for example, makes rail more expensive but greener for a particular journey at a particular time. I doubt whether it makes the difference which would make it always the case that the more expensive option was the greener, particularly as air is nominally underpriced because it doesn't pay enough emissions tax, and rail is underpriced because it benefits from state subsidies. So you can either delve into full analysis of all the negative externalities of a particular journey taken by all the possible means, or you can be pragmatic and say the less you consume, the less you fuck the planet. That's why not taking the trip at all is the best option.

I'm not sure what you consider to be opinion. When I say something is the case, I'm presenting the current state of my knowledge [AFAIK]. Correct me if I'm wrong.
When I say what should be done, I'm presenting an opinion [IMO]. Persuade me that I'm wrong.