This has got to be the reason he was retained. Of course Raiola only had one year with Frost and coming from the NFL he may have seen huge deficiencies in the program. Judging by Frost's total lack of attention and particularly lack of attention to details, I could see this being the issue. Kind of hard being the new guy and insisting on wide scale changes in the S&C program and how the line blocks. Also- some of that could be on Whip as well. If someone could write a book about the behind the curtain aspects of the Frost era, it would probably be an interesting read.
With respect to S&C different player positions need to be trained differently. Also each individual player's needs vary somewhat. Stretching and strengthening go together and training the whole body as a unit. Some will argue against stretching for building strength but that has to do with timing and the amount done and duration in relation to times. People recover somewhat differently. There's got to be some tailoring going on for each person. A lineman trains differently than a receiver, etc. Speed, power, agility and a number of things to consider.
It's hard to say what has been going on or not going on. Perhaps the attention to detail wasn't what it needed to be. Strangely enough, one's breathing habits can play a significant role restricting playing at a higher level. Things being marginally different can have a considerable effect. I don't know...To me Scott appeared and acted tired much of the time. Lack of sleep and other possible considerations really does affect one's ability to function at a high level. It's a demanding profession.