Well, I'm only having this issue since the new GE was put in place. If I put "strictly follow depth chart", then I expect, that the coach uses the depth chart, until not one of those players is availabel anymore, and screw the consequences. If that is not possible, then eliminate that option (since then I can't see any difference to the "strictly follow until 4th quarter" option)!
I realize that the problem (and hence the algorithm to calculate it) probably is quite tricky. Not knowing anything about your algorithms or logic, I can't give you any advice, though. But before the change, the coach rarely used a player not listed in the depth chart, regardless of the substitution option, or whether it was a blowout or not. Now he does it regularily (3 ot of my last 4 games). With this behaviour, it is quite tricky, to get meaningful training minutes.