At the meeting, Team NZ chair Sir Stephen Tindall said they were now willing to be flexible about the other options as they had taken into account public opposition to moves to extend work into the harbour.
A statement released later, however, indicated the team's disappointment that the Halsey extension option had been taken off the table.
"It seriously restricts the ability for the marine industry to benefit from the berthing of the super yachts and the ability to extract maximum economic benefit.
"The final plan for the Wynyard Basin option will need to re-incorporate the lost super yacht berth age within the event perimeter. We will continue to work constructively with Council and Government to progress the plans.''
There was a worry that Team New Zealand may take the event away from Auckland, to Tauranga or even offshore to Italy.
However, Team NZ chief operations officer Kevin Shoebridge told the Herald even though their preferred option would not happen, they would be working with the options available and there would be no moves to take the America's Cup away from the city.
Mayor Phil Goff's preferred option is the clustered base at Wynyard Basin, which would cost just over $130 million, plus an $18 million relocation cost as well as $90m of unbudgeted money needed for downtown projects.
"The council has agreed on a preference for the Wynyard Basin option which clusters bases around Halsey Wharf, Hobson Wharf and Wynyard Wharf East to take into further negotiations.
"This option will allow a great village atmosphere, is less intrusive on our harbour, around $40 million cheaper and eight months quicker to construct.
"I want to thank Emirates Team New Zealand for their flexibility. There is strong council support to make the event successful and memorable, and to ensure it provides a lasting legacy for Auckland and New Zealand."
It would take about 10 months to construct and would displace one tenant that would need to be relocated.
This option is also favoured by the Council's Panuku Development Auckland group as well as Team NZ.
Ngāti Whātua Ōrākei spokesman Ngarimu Blair said it was good to see that "common sense has prevailed" but the iwi was still dubious about any option that involved extending further into the harbour.
"Over the last 120 years, bit by bit, we've seen the Waitemata narrowed," Blair said. "We're going to take a lot of convincing that any more extension northward to the North Shore side is of any benefit, firstly, to the mana of the harbour, and secondly will leave something of value to all parts of the Auckland community."
Michael Goldwater, spokesman for protest group Stop Stealing Our Harbour, said the group was also opposed to the council's preferred option.
"We don't think it's a good idea for environmental reasons, and we don't think that sticking a whole lot of sheds on the end of a concrete wharf is the best thing to do from an urban design perspective."
The group believes any projections around economic benefits of the cup are likely to be highly overstated - as is talk of the development's "legacy".
"We already have a legacy - which is an intact Auckland Harbour."
The Wynyard Point dispersed base option would take up to 14 months to build and also involves the relocation of existing tenants - businesses - in the area. It would cost about $170 million, plus the $18 million relocation cost.
Shoebridge told councillors there were some issues with the Wynyard Point dispersed option - favoured by the Government - including that at least two base spots would see a low-water issue.
A dispersed base might lack a cohesive village atmosphere also, he said.
Speaking about how the event was hosted in San Francisco, he said: "It was pretty fragmented ... and it didn't draw a lot of the public because of that.''
For the international crowd watching the event, it was fine, he said.
"Locally, it suffered. A lot of people in San Francisco didn't even know the event was on.''
The Heart of the City also favoured clustering the bases and was vehemently opposed to the Halsey St Wharf extension.
A spokeswoman said clustered bases would be a more practical and ideal option that would meet the teams' needs as well as be economic and meet the public's needs.
The Waitemata and the Devonport-Takapuna local boards were also against extending the wharf into the harbour, but did support having the Cup in Auckland.
Waitemata local board deputy chairman Shale Chambers said the clustered bases would be a "pragmatic solution" that would save up to $50 million and provide a legacy for the city.
