Ecto 3.10 (which I hoped to be out by now, but alas it isn’t) will include Ecto.Changeset.get_assoc, which in combination with Ecto.Changeset.put_assoc should make modification of assocs a bit more comfortable.

Is there a reason to go with nested embeds? These make sense if you have multiple fields per row, but you don’t seem to have that. I’d consider using checkboxes to toggle and transform the resulting list to a nested structure only on submit. I’ve a small POC for a checkboxes component and there’s a fly.io blogpost for something similar:
Scratchpad | Benjamin Milde
Making a CheckboxGroup Input · The Phoenix Files

There it is!

https://hexdocs.pm/ecto/changelog.html#v3-10-0-2023-04-10

Based off of the guide you’re trying to adapt and your join schema, maybe try something like this?

def handle_event("add-topping", %{"topping_id" => topping_id}, socket) do
  pizza_topping = %PizzaTopping{topping_id: topping_id}

  socket =
    update(socket, :form, fn %{source: changeset} ->
      existing = get_change_or_field(changeset, :pizza_toppings)
      changeset = Ecto.Changeset.put_assoc(changeset, :pizza_toppings, existing ++ [pizza_topping])
      to_form(changeset)
    end)

  {:noreply, socket}
end

defp get_change_or_field(changeset, field) do
  with nil <- Ecto.Changeset.get_change(changeset, field) do
    Ecto.Changeset.get_field(changeset, field, [])
  end
end

See: Adding tags to a post | Ecto.Changeset

There seems to be an understandable disconnect between Ecto and LiveView that likely exists because Ecto predates LiveView and was designed for the stateless paradigm of HTTP requests handled by conventional controllers. Subsequently, there is no default interface/function to incrementally build/add to an existing association within a parent changeset. Basically, something like Ecto.Changeset.add_to_assoc/3 doesn’t exist – but if it did, we could then do something like this:

def handle_event("add-topping", %{"topping_id" => topping_id}, socket) do
   {:noreply,
     update(socket, :form, fn %{source: changeset} ->
       changeset
       |> Ecto.Changeset.add_to_assoc(:pizza_toppings, %PizzaTopping{topping_id: topping_id})
       |> to_form
     end)
   }
end

Yes, I’m starting to think that might be good way of implementing it. Thanks!