By the time it is all said and done,... I will have spent close to $100,000 for a Level 5 trainer, who is gonna make $19000 a week,...
So by that same logic, let's say you have a C being paid $10k a week. You look on the transfer list for a better player, and let's say you have to pay about $2m for a C paid $20k a week.
So you've just paid $2m for someone who's going to get paid $10k a week more. It doesn't make sense in itself, but you have to look at the other effects - in this case, more chances of winning games, more home fans, more home revenue, more chance of being promoted which brings more revenue, etc etc. By the time you factor all these things in, this player will probably give back all the investment in a couple of seasons.
In your example, the higher level trainer will mean that your trainees train faster, which means that when you come to sell some/all of them, they will sell for more, sometimes substantially more depending on what skill set they have. In the meantime, you get to use those players in games, and because they have trained faster you have more chance of winning games, more home fans, more home revenue, more chance of being promoted etc etc. Factor all this in and the $100k investment pales into insignificance.