The defence giant has given its clearest signal yet that it aims to build a whole new generation of Royal Navy warships at a proposed, "world-class facility," at its Scotstoun yard in Glasgow.
Company bosses, however, admit their preferred scheme would cast doubts on the long-term future of their second Clyde yard, the historic Fairfields in Govan, which they now describe as "sub-optimal".
BAE Systems and the UK Government will not announce a final decision on the factory - state-of-the-art Type 26 frigates, or Global Combat Ships - until shortly after September's independence referendum.
And Ministry of Defence officials will have a huge say over whether BAE Systems builds the ships in Scotland and, if it does, whether it does so at the proposed new facility in Scotstoun or, under a Plan B, across both Glasgow yards.
However, BAE Systems director of business and transformation Charlie Blakemore makes little secret that he would like to see the Type 26s built under a single roof in Scotstoun.
He said: "The Scotstoun facility requires more investment but delivers significantly more benefits.
"There is an affordability issue in the initial stages, more construction needed, more facilities work, but it will provide a capacity that is truly world class. We will then be able to compete in a more level playing field."
Investment at Scotstoun would include a 330m-long new dock hall, one of the biggest industrial structures in Scotland and capable of building two ships at once - all indoors.
Such a facility would churn out warships a third faster than across both yards, making the navy's new Type 26s "significantly cheaper", said Mr Blakemore.
That will put BAE Systems in a position not only to produce frigates for the Royal Navy, but to offer competitive terms to foreign navies too.
Brazil, Indonesia and several other countries are said to be interested in the technology and, if the price is right, in the finished product.
The company has not ruled out Mr Blakemore's Plan B. This would see parts of the frigates build at one yard before being carried, expensively, on barges to the other.
Even that proposal would cost "north of £100m" in investment, Mr Blakemore said. One of Govan's existing sheds could be extended - but it would still be too small to hold a frigate - so either a bow or a stern would stick out of the hangar-like structure.
"That is suboptimal," added Mr Blakemore. "The best shipyards are doing all their work under one roof, as we envisage at Scotstoun."
Unions have cautiously backed the proposals for expanding Scotstoun and, potentially, phasing out Govan, despite huge sentimental attachment to the iconic southbank yard.
BAE Systems will need the same number of workers to make its ships however it organises production, across one yard or two.
But GMB steward John Dolan stressed that the Scotstoun option offered the best long-term future.
The Labour stalwart said: "If we stand still, we will fail in five years. A frigate factory in Scotstoun would be tremendous.
"The facilities would be first class and would make use of a more modern 21st-Century yard able to compete with foreign shipbuilders. Right now we are way behind."
Mr Dolan and unionist politicians have long argued that the Type 26 contract will only come to Scotland if there is a No vote in the referendum.
Last night he said: "If the vote does not go the right way, the decision will be made for BAE Systems because the UK government won't order ships in what will be a foreign country.
"Can you imagine the situation in Portsmouth if the MoD decided to build ships in an independent Scotland? Do you think they would be delighted?"
Industry insiders stress that making the Type 26s in England would involve a huge and expensive operation to reskill and retool BAE's Portsmouth yard, currently slated for closure.
Mr Dolan said he thought whispers that England couldn't make the ships - except at punitive cost - was "insulting" to his Portsmouth colleagues.
Mr Blakemore, meanwhile, stressed his company's decision, announced late last year, to shut Portsmouth and earmark the Clyde for the frigate contracts had nothing to do with the referendum.
He said: "The reason we have chosen the Clyde is because of the skills and the capabilities. This is all based on industrial reasons, not politics."
Asked if BAE Systems could make the Type 26s south of the Border if Scotland votes yes, he said: "It is fair to say anything is possible. It is just there is going to be a cost. It's an option we have not explored in great detail.
"We do have the same skill sets in Portsmouth as we have here. They are just not available in the same depth and numbers."
The SNP argues it would be impractical for the Royal Navy to insist its warships are made in England after independence.
Deputy First Minister Nicola Sturgeon welcomed the proposed investment at Scotstoun - but insisted that Govan must be safeguarded too.
She said: "It is ironic that we have Better Together leafleting in Govan saying vote No to save Govan."