This season is different than the season you're referring to for Pogba. We need every single point at the moment. Conte had the chance to be more 'flexible'.
It was Conte's second season. Roma had a 10 game clean sheet winning streak and looked like the real deal. We had to re-affirm that our miracle season was not a fluke. Surely it was not as tight as it is for us now but he didn't have Bayern flexibility either.
With Fergie, he had to win the league with a shit squad, was very short on midfielders and instead opted to bring scholes out of retirement than play Pogba. Did he win the league? Yes. Did it affect Utd in the future? definitely. Could he have won had he played Pogba? probably. The pogba case (regardless of how good or bad rugani is I have no informed opinion about the matter) demonstrates the principle; namely that a coach can be wrong about benching a promising player even though the team won the match/league.
You are right in pointing out the difference between how promising pogba was and Rugani is. If Rugani does get upset and leaves us and does turn out to be a very good player ( meaning that we could have still won had he played) and allegri continues to not give him chances then this could prove to be a mistake by Allegri. However, given that it is unlikely that he gets that upset and unlikely that we would let him leave and unlikely that Allegri wont give him many chances in the future then I do not think that it will actually be a mistake. Allegri will likely give him chances and this will prove to be nothing.