"In fact, his previous endo said our goal was to completely suppress his adrenal function because it was easier to calculate/titrate a complete replacement dose, then to figure out what he was making already and replace the necessary remainder."

In having read that it has to be said that even if a child can make "some" cortisol, when they partially replace the level they "think" is needed to top up, the adrenals still have to do the rest of the work, and once the levels of cortisol are sensed by the pituitary, what will inevitable happen is that the adrenals WILL attempt to make the remainder, but the portion that they make will be reduced again because they can only ever make "part" of what they are supposed to make anyway.  Be that a top up amount or the full amount.  So the Doctor is right when he states that your best off shutting down the whole thing back replacing the total amount a child would need.  The problem being that with children that can make "some" cortisol, it takes a great deal longer to pick up problems than those that don’t make any at all.  The ones that don’t make any at all get into elevated androgen levels in no time.  The one whom can make some will have problems when they grow out of a dose.  That’s because slowly over time, the adrenals step up output as the pituitary senses the lack, and they can be running on making cortisol full time and infact end up with much higher cortisol levels than kids who are on the full maintenance dose that it takes to shut the HPA axis up.  

Shutting HPA offf IMHO is going to be much better than having the child continually trying to make the extra bit of cortisol on top of the amount they are given as they will never quite be able to satisfy the puituitary’s demands for it.  Saying that I think that even if they are receiving just a smidgen over what they should to do this, this is much better than being in awhat has to be a constant manufacturing of cortisol 24 hours per day.  Such a child would have growth issues I am sure.