There could be many reasons. Maybe it helps him find the mal-contents. Maybe it helps him find those team players. It may not about conditioning at all, or little to do with conditioning. Do you know anyone who was actually cut, from the team, due to not making the time?
Maybe once practices starts he does not want to have to spend time on conditioning. I know of more than one d3 college that required players to run a mile or two in under a certain period time to be able to start practices, with the team. If you couldn't you were running during practice. Practices are fast paced and running from station to station. Little to no standing around.
Unless we know the motivation, there is no reason to point fingers or judge the coach. As others have said, everybody just needs to understand what they can control and worry about that.