The fact that you can buy any ship in the game with real world money at all is the problem.

These people are paying to remove that part of the game which blows my mind

Yeah for people who actually enjoy putting the work in it doesn't make much sense, but for some people who play video games it's not about the getting it's about the having. The problem is that in this case they can use real world money to have better stuff without having to work for it, giving them an advantage over other players who are poor or don't want to pay for their ships. If this was 48k for just ship skins and it didn't affect gameplay at all then it'd be pretty stupid still, but I would at least concede that the average person doesn't have any disadvantages if they only pay the 45$ for the main game and don't need to pay thousands of dollars to reasonably compete with players who have bigger wallets and less impulse control. But that doesn't seem to be the case here since different ships have different stats and abilities afaik. This essentially means that rich people (or gambling addicts which are their own can of worms) can unlock more of the game and perform better faster than people who only pay for the base game.