IV.41 party!
Yes, if a player is listed as both a starter and backup, he loses 5 minutes. It is absolutely possible to go over 48 minutes by playing a player as a backup at multiple positions, though it is impossible to get more than 43 minutes in a single position. On the bright side, since it's a walkover, your players may still be injured! But don't field a blank lineup or they won't get any minutes at all. I think that's pretty much all the unusual stuff involved in walkovers.
So wait, how do you get 48 minutes for one player in a walkover?
I listed one trainee as starting PG, and then backup and reserve SG, and he only ended up with 43 minutes total.
Should I have listed him as backup at 3 more positions so he'd get 49 minutes?
You can, but not in one position. Maybe not even in two. I think you'd have to do something like starter A, backup position A, backup position B and that I think gets 51. I'd have to find a couple of the games I had saved where I'd worked out the details, though. The main thing is that you'll lose five minutes if you have a guy be a starter and a backup, regardless of any positions, but I am 99% sure that you don't lose any extra minutes if he backs up multiple positions.