The game leaves many open paths, it could be more restrictive.
In a sense, we are trusted by the creators to make sensible decisions most of the time.
This is something I liked about BB from the beginning. I know I am stupid to think that but I believe the game creators didn't want a game where the player would be assisted too much in his decision-making and babysat. Instead, they assume a pre-conception that the player is an intelligent individual, capable of judgement. Of course, the player will make mistakes, sometimes many mistakes. As an intelligent person, he will be able to identify and correct them after a while. It's normal to make mistakes, it's part of the learning process. You make mistakes, you understand them and correct them.
There could be a hard cap on training, it would make sense, physical limits, age, etc... all this concur in stop skills improvement at one point.
But there is not. You are trusted to understand that it is not your interest to continue training a player past some point.
What follows is from a franchise point of view. NT players make this irrelevant but let's forget about NT players for now.
You say it yourself. Salary too high. Transfer fee too low.
Your question is why can't I keep the player when it should be why should I continue to train him ?
This situation arise from the fact that you didn't identify the consequence of this extra training. Or that you chose to ignore it expecting a rule change.
The game treats you like a grown-up. It didn't stop you from continuing his training. You were expected to think about what you were doing.
You are empowered and given room to do your own way and your own stuff. Some like to win, some like to train, some like to trade, some like to test the GE, some like to flood the suggestions forum ^^
BB isn't a nanny state with rules designed to protect you from hurting yourself. You are an intelligent individual with free will. Go, live, make your own mistakes, learn. Yes, boiled water burns, I warned you, now you know :)
Because it was possible to overtrain doesn't mean that you had to. You are reversing the problem when you ask, now that my player is overtrained, why can't I... ? The problem should have been thought about before in anticipation. This is what managing is about.
It makes sense to be able to overtrain a player. It is based on a concept that is a cornerstone for the game genre. You can do stuff, even some very unwise stuff. It's your role to make the calls.