> In which situation does the end user not pay for everything?

If you want to get technical about it the field of economics addresses this question. Its called Tax Incidence. The short story is that the side of the market that has the least elasticity of demand (IE, they respond to price changes the least, and don't buy more or less because of price changes) is the entity that suffers the costs of taxes and gets the benefits of subsidies.

Intuitively this makes sense. Imagine if there is a luxury good that you don't need. If taxes increase significant on it, you may just choose not to buy it. That has a high elasticity of demand. Meaning that the tax incidence isn't going to be on the consumer and will instead be on the produce.

Whereas, think about food. People don't eat much more or less based on how much it cost. You can't physically eat more than like twice as much, and if you don't have any you die. Meaning that its a low elasticity of demand, meaning that the consumer pays the taxes.