This is another of those things where there is no right or wrong.
I have done both shoulders and brisket both ways, and I prefer wrapping to catch all the juices, which I then mix back into the pulled pork. And wrapping lets it cruise right through the stall.
But... I wait to wrap until after the bark has had a good chance to develop, and since I use a brown sugar based rub and kick the heat up to about 300° when I foil, the bark continues to darken even while wrapped.
As far as the bark softening during the foil, the bark is going to soften a little bit anyway once you pull the pork and mix it in, so it's not a big deal to me. Maybe the brown sugar rub makes a difference, all I know is I always seem to end up with plenty of bark and have never had a complaint.
Anyway, that's my story and I'm sticking to it!