The latest report from the Institute for Fiscal Studies, forecasting years of additional austerity if Britain votes to leave the European Union, has uncannily similarities with the one it published during the Scottish independence referendum – right down to the former Labour chancellor Alistair Darling saying it makes the case for remaining in the union unanswerable. Mind you, this time the SNP agrees with him.

Just as the prospectus for Scottish independence was crushed by the sheer weight of unionist statistics, so the Brexiteers appear to be losing the argument, day by day, report by report. It may be the wrong argument, as they claim. But the relentless assault of fiscal negatives has put the Brexit campaign so far on the back foot it's resorted to accusing the IFS of being in the pay of Brussels. “The propaganda arm of the EU” as Vote Leave unwisely put it.

The Institute for Fiscal Studies is, of course, the most respected think tank in this field, renowned for its political independence and for being the “gold standard” on taxation and welfare. It is often fiercely critical of the government of the day. It savaged George Osborne's benefit cuts recently, saying they would plunge 2.6 million children into poverty. This is why people tend to believe what the IFS says.

And what it says is that there will be a £20-£40 billion black hole in the nation's finances if Britain votes to leave the EU, depending on whether or not we join the European Economic Area with non-EU countries like Norway. Either way, the cost of borrowing will rise, house prices will fall, GDP will flatten and trade will shrink. The IFS isn't quite as pessimistic as the Treasury on how rapidly national income will decline, but it is adamant families will be a lot worse off out than in.

With shades of the row over North Sea oil, the IFS also describes as “absurd” the Leave campaign's claim Britain would be £16bn a year better off – £350 million a week as the Brexit bus says – because we would no longer be paying into the Brussels coffers. It would be less than half that, says Paul Johnson the IFS director, and wouldn’t compensate for the economic contraction caused by leaving the EU. If we join the EEA we'll have to pay for access to the single market without having any say on how it is run.

Naturally, the Brexiteers are furious at what they call a negative and one-sided assessment that mendaciously discounts the potential benefits of Britain being liberated from Brussels bureaucracy. They say the eurozone's growth rate is flatlining compared with countries like America and China; that Britain would be free to negotiate trade with the booming rest of the world. Stop running down Britain, say the Leavers, echoing Alex Salmond during the Scottish referendum debates.

But the problem for Leave, as with Yes Scotland, is that it's not possible to provide credible figures in a prospectus for the unknown. Leaving the EU, like Scottish independence, is essentially an act of faith: a belief Britain, the fourth largest economy in the world, could survive and thrive it if was no longer held back by Brussels. And it certainly could – but the problem is getting from here to there. Radical change always comes wrapped in uncertainties and discontinuities.

What the IFS, most economists and the Treasury are saying, essentially, is that Britain would become an investment risk while it disengaged from Europe. The markets would demand higher interest on loans to Britain, which is why austerity would be prolonged and the deficit would grow. Meanwhile businesses, many of which located in the UK to gain access to Europe, would consider relocation. Outside the customs union, British exports to Europe could become more expensive.

The Brexiteers insist all these things could be ironed out. Interest rates would normalise; there could still be free trade with Europe; and firms would think twice about leaving. But what they can't dispel is the threat of financial instability. This is the black hole into which any referendum fought purely on economic advantage will inevitably sink. It is almost impossible to quantify any direct benefit from leaving the EU – apart from the contested savings from Britain's budget contribution.

This is the essence of Project Fear. The objective is to frighten the middle classes, struggling families and older people with the prospect of economic disruption. It worked in Scotland and it seems to be working for Remain in Europe. Recent polls suggest pensioners and homeowners, many of them Conservative voters, are now turning against the idea of Brexit. The day-by-day stories about how holidays will cost more, terrorism will get worse, relatives abroad will be isolated are built on the premise of financial risk.

I'm not saying the IFS is a willing collaborator in the Remain campaign, or that it has politicised its figures. It's just that, as it did on Scottish independence, it is looking solely at the short to medium term. It isn't concerned with wider issues like the austerity economics being imposed by Europe on countries like Greece. Nor is it bothered by any lack of democratic accountability in EU institutions. Its focus is purely on the virtual certainty there will be a price to pay for leaving, whatever the long-term gain.

I take no issue with the IFS on its numbers. It has no axe to grind and it certainly isn't bought and sold by Brussels gold as has been claimed But there is an in-built conservatism in its narrow fiscal focus – a straight-jacket that makes all change seem unacceptably dangerous. If and when a left wing government were to win a general election, the IFS response will no doubt be very much the same. It will argue anti-business policies will lead to a flight of capital, that increasing taxes on the very wealthy could reduce the tax revenues (as Nicola Sturgeon has accepted). The IFS would also warn attempts to tax business more highly or to restore trades union rights would damage GDP because many businesses would leave the country.

The message is that Project Fear works. And the lesson for the Scottish independence movement is this: referendums may be the accepted method for resolving issues of sovereignty , but they also tend to favour the political establishment, if only because it can portray any change as a leap in the dark.

If and when another independence referendum is mooted, the Scottish Government will have to be absolutely sure it can win it. I'd even go as far as to say that, ironically, Scotland would have to be effectively independent before a referendum could be won. The Scottish Parliament will have to acquire independence policy by policy, tax by tax, until a referendum on independence becomes largely a recognition of reality. Only then would the logic of Project Fear be reversed.

It's a sobering lesson for the independence radicals, but it confirms the SNP's policy of gradualism is probably the only way. Referendums are just too scary for modern electorates, whose fear of losing what they have will always trump the hope of what they could gain.