The Rabbanut seems to not necessarily work on any given set of standards.

In the case of shmitta, the Chief Rabbinate has decided to allow the use of hetter mechira produce and deem it a shmitta solution. Some local city Rabbanuts have decided that despite the official Rabbanut position, they don't want hetter mechira to be used in their cities.

In Netanyah and Herzliya, the Rabbanut administrations have instructed local hotels to not purchase vegetables from hetter mechira produce, but to buy produce from abroad (often this means a bit from Europe, some from neighboring countries like Jordan and Egypt, and more from Palestinian Arabs in areas like Gaza and elsewhere).

This upset many people, specifically the farmers association. If the Rabbanut, and the army already announced it will be doing so, will be directing purchasers to imported produce, that would be a major blow to Israeli agriculture and local parnassa.

It almost seems like what's the point of the hetter mechira, which was meant specifically to avoid causing tremendous economic damage to Israeli farmers, if the Rabbanuts wont allow its use anyway and will make the major purchasers buy from the competition?

Chief Rabbi Dovid Lau responded saying he has instructed all the local rabbanut offices to approve the use of hetter mechira produce, for normal basic kashrut levels (meaning, a hotel or restaurant that is mehadrin kashrut, will buy imported produce or some other type but not hetter mechira, but hotels and restaurants under regular rabbanut should be using hetter mechira).

Even more interestingly, Rav Lau announced that any place that has a complaint that the local rabbanut is not authorizing the use of hetter mechira, the situation will be looked into. While the situation is being analyze,d which can sometimes take time, in order to avoid the hotelier to be hurt by the process, as what will he do in the meantime, Rav Avraham Yosef will be appointed to be able to circumvent the Rabbanut and give a temporary hechsher on his own to such places until the issue of the rabbanuts approval will be worked out.
source: TheMarker

That's pretty cool. Instructing the Rabbanut what to do, and then setting up a channel to circumvent them when they won't listen (i.e. he knows in advance there will be some who won't listen to the rules).

Perhaps, seeing this, this is why some people are so worried about the possibility of local rabbinates, made up of rabbis certified by the chief rabbinate and following the basic guidelines of the rabbinate, being given authority over conversions. If there is no set of standards that must be followed within the organization, then any city rabbi can do whatever he wants and demand or allow whatever he prefers. If the Rabbanut officially allows hetter mechira but any city rabbi can decide he doesnt allow it, then perhaps the same can happen in conversions..