The extra charges you have encountered are taxes etc. They are shown in the top right hand corner as a running total when you are choosing your tickets. Try the initial booking again and you'll see what I mean - and you'll see that Jet2 hasn't gone out of it's way to highlight it.
This covers the requirement to show all taxes, fees etc but also means the "big numbers" are lower.
It's perfectly legal and viable and no different from a lot of other airlines, but I think it shouldn't be done this way. Little underhand for my liking.