I am not sure what you mean. The percentages only effect the training. But if you want to avoid the lowered training, you have to play guys in positions they may not excel at, and your team will play beneath it's max ability. Plus, I was training mostly one position training this season, and I wanted to get three players fully trained, so I would also play that trainee the full 48 minutes, reducing his effectiveness further.
Sorry if you already knew what I meant, it is likely I am the one confused here, lol.