I think that the idea is to make a trade-off between a (free!) upgrade of your player and the unavailability for a few days. I mainly play to be competitive in association matches. Since the 3 day training is finished before the next association tournament, it seems worthwhile to do the training. In this phase of the season (group matches CL and easy cup games) I can afford to miss a good player for a few days.
For longer trainings I don’t see the point of investing. The costs are comparative to manual training in terms of % gained. In manual training you can better pick the skills and you won’t loose your player for many days.