I think
Drannith Magistrate will be played like most hatebears, both in deckbuilding and impact after it resolves. The decks that add it do either because it impact their metagame in a favorable way or because it's on theme (eg. wizard tribal control). Once it resolves, it probably has the same impact as
Hushbringer in most groups where hushbringer sees play. It builds political alliances between players that are equally impacted, for example the
Syr Konrad, the Grim and
Meren of Clan Nel Toth players would have a shared interest in removing the hushbringer, but a
Kruphix, God of Horizons player would have interest in protecting it. The main difference with magistrate is that most players that depend on their own commander will have incentive to remove it unless it's demonstrably saving the table, for example by keeping
Zada, Hedron Grinder from storming off or
Thrasios, Triton Hero from having a sink for his infinite mana.
Like most hatebears, it delays most decks at low mana investment but generates no direct CA. I do believe it creates virtual CA+tempo by delaying/preventing commanders but short of a deck dedicated to resolving and protecting the magistrate, I don't think it will be over centralizing. The closest that I could see for it being centralizing would be in something like
Teshar, Ancestor's Apostle+hatebears+eggs(which I may build now that I think about it), but I doubt that's going to be common.
I disagree with the comparison to
Prophet of Kruphix based on to the scale of the average advantage. PoK was effectively a massive tempo swing that could generate game-winning opportunities quickly while also helping protect itself via untapped mana. As long as the players all had creatures or instants, PoK because a focal point for killing/stealing. The tempo swing from magistrate starts smaller, but can be increase if the opponents generate most of their CA or tempo from the commander itself. I agree that this is more back-breaking to decks with engine-type commanders like Nin, Feather, Zada, or Chulane (and honestly about 75% of my decks due to silly themes or self restriction). However, even against those decks I don't think the quantity of CA+tempo is comparable. If it sticks around for 1 full turn cycle and stops three commanders that generate around 2 CA/turn, then maybe the tempo swing is comparable to PoK at around -6 CA for your opponents. But then the Nin, Chulane and Najeela players have made a pact to end your life.
However, due to the asymmetric nature of the effect it's likely that most groups (extrapolating from my own) will remove it as soon as they need their commander. I could see theft effects being used instead, but it's still a 3v1 situation with removal vs protection. I don't think it's anywhere near ban-able.