I agree blowouts don't always cause missed minutes, but they can be a factor. There are more factors I believe when minutes are missed despite the standaard settings to get 48 minutes, for example the skills of the player (if he's very unsuitable for the position he is trained in he has a higher chance to miss more minutes), or possibly stamina.
The fact is, despite setting the right settings there are situations besides fouling/injury that cause a player to miss minutes. Not all of them can be fixed for a specific game, but you do have some influence on blowouts. That's why people mention it, it's not always advisable but it is an option to possibly reduce the chance for missed minutes.
That said, if you're willing to sacrifice game performance or even gameshape, a better way to prevent minutes loss is to just dress 5 players. Then there's no-one to sub in for your trainee. This has many consequences though, but if training is your sole priority I think it's the safest option.