The core devs have always been pretty open about how they don't want lemmy.ml to be "the flagship instance". To them, it's just the instance that they run, and so happens to have the history of being the biggest instance back when lemmy was growing its user base.

They actively encouraged new/other instances be created and pushed new users during the reddit migration to other instances, rarely listing their own instance in the list of recommended instances on join-lemmy.

So it's not the flagship, and intentionally so. And while lemmy.world is the biggest by far, it is also arguably not the flagship either due to the lack of having the core devs or contributors as admins of that instance. All of which means lemmy has done something most other platforms have struggled with (I'm looking at you mastodon.social!), which is flattening the power structure amongst the devs and admins such that there is no real flagship, an all around good thing IMO.

There is no main instance, that's the whole point

No. lemmy.ml used to be the biggest instance with the most communities originating there. (And the instance launched by the developers.) It has been the flagship instance. But it's a thing of the past. Just have a look at the statistics. For example here or here. The biggest instance currently is lemmy.world with about 5 times the active users. And since the reddit exodus, most of the active communities have been opened on other instances.

For better or for worse (obligatory remark on how in a federated model there should be no “main” or “flagship” instance) that would probably be lemmy.world on the sheer number of users alone?

It's run by the devs. That's it. It is neither the largest nor the most engaging instance - but at least updates are done pretty quick.

There is no such thing as primary instance

You seem to be missing the point of decentralization.

It’s probably Lemmy.world

But the beauty of federation is that it’s about the size of the fleet, not any specific ship.

Lemmy.ml is like Delaware. The First State.