My understanding of the "back to sleep" issue is that babies are not to be put to sleep on their tummies, away from where someone is watching them.  Regardless of the type of bed, the feeling was that baby would be basically rebreathing its own carbon dioxide, leading to a greater tendency towards apnea, and therefore SIDS, since no-one would be alerted to wake the baby.  We do not say that a baby should NEVER be on its stomach, but that someone should be nearby and alert when baby is in that position.
We also say babies can sleep on their bellies on moms' bellies, since the constant readjustment of both would keep joggling babies in their sleep to make sure they don't stop breathing.

A baby under bili lights in a nursery is not usually connected to a 
breathing monitor, but he is being continuously checked by his nurse 
regarding a number of parameters.  This contancy of his nurse's 
attention and awareness is what is usually missing when parents 
put their baby to bed in a crib, on his stomach.

I seem to remember long ago having it explained to me that the 
we needed to provide the baby with exposure to as much of the body surface as possible, to maximize the benefit of the lights.  If  the baby wasn't turned over to back to front, then back again, throughout the day, would that mean the baby accrued only half the benefits?  

   And since the amount of time mom or dad can hold their baby is limited, since this is time away from the lights, aren't their "hazards of bedrest"  that would come into play if the baby were not changed from position to position throughout the day?

I think, also, it is a matter of weighing the risks.  The baby is being treated for a known risk, with a potential for brain damage.     I don't know at what level your hospital starts to treat, or what this kid's bili was, but if it's anything like mine, the bili is pretty high before the kid goes under lights (18 and rising), and you want to do everything you can to start bringing it down, (short of insisting on formula, which fortunately, my hospital doesn't, unless baby is still losing weight, and mom is already pumping for supplementation).  Which is the greater potential for damage at this time:  1) that the baby's bili will still climb, or at the very least take a while to start dropping? or 2) that the baby will succumb to SIDS in the nursery?

You're right to question the doctor's response. It was the wrong response.  But there are still good reasons to put the baby on his stomach in this situation.

(While writing this, by the way, I did call our nursery to ask what our practice is.  They do turn the babies at least from back to side, and side to side, because the more skin they expose, the faster the jaundice resolves.  While they try to avoid a prone position, it is often the most comforting position for an unwrapped baby, and they use comfort as one of their guidelines.  Finally, they feel the threat of lying on the stomach is minimalized, since the baby is unwrapped, in constant sight, and therefore not likely to stop breathing and turn blue with no-one noticing.)

Sincerely,  Chanita