My guess would be he has it setup as a "Tandem" rotation with the RP or AAA guys as Tandem 1A and the better pitcher as Tandem 1B.
As for pitch counts, to get the "long relief" pitcher to hit their 95-105 as desired, make sure they are not being pinch hit for (you can uncheck their PH box in advanced settings) or set your PH to 1. Also, to get them to pitch to their limits, set their "call pen" number to 1 as well. This will keep them in the game longer as they won't be pulled for another RP.
The only thing I can think of as to why a pitcher was left in for 96 pitches if you had the target at 40 and max at 45 would be that your relievers were not available until a certain inning (5th inning perhaps) and since no one was available to relieve your pitcher until a certain inning, Sparky let him throw that many pitches. Check your Advanced Settings to see when your guys set for Long relief are available.