The big difference between a top 50 D1 and a top 25 D3 is the time involved in the sport.
Although I'd like to believe that, I think the reality is that those top 50 or so programs end up with the best athletes overall and that factor, more than time spent practicing is what drives the difference. I do agree that once you drop down past those top programs the differences, if any, amongst a wide range of the smaller DI, DII, and stronger DIII programs are not significant from what I've seen.
As far as time invested, if I compare what my kid (DIII) did this year vs some of her former TB teammates (now small DI's) did, there was very little if any difference in time spent per week in the weight room, practicing, etc. The DI's play a longer season, but in terms of hours/week, it seemed pretty comparable other than travel time here and there (DI's had some more overnight trips and missed a few days more of classes)