Professor Jim Gallagher said Scotland could "surely avoid" having to join the euro or the open-borders Schengen area when negotiating EU entry.
Prof Gallagher, formerly the UK's most senior civil servant responsible for devolution, was appointed last week to advise Better Together on policy and strategy.
The SNP claimed Better Together "scare stories" about Scotland being forced into the Euro and the free travel area had been debunked by their own expert.
Writing last April on an academic blog run by Edinburgh University, Prof Gallagher said that, although there would be many uncertainties in the event of a Yes vote, it was possible to make "an educated guess about how things might turn out".
He said: "For example, it seems pretty likely that Scotland would be an EU member state, probably after an accelerated set of accession negotiations. Precisely what the conditions of membership would be is not quite so clear, though immediate requirements to join the Euro or Schengen agreement can surely be avoided."
The comments appear at odds with those of Better Together chairman Alistair Darling.
In July, the former Labour chancellor suggested independence would mean adopting the Euro.
He said: "If the nationalists don't want us to join the Euro or Schengen that would mean negotiating with 28 other countries an opt-out from both obligations - something no other new EU member state has done."
In a statement issued by Better Together, Prof Gallagher said since he wrote the blog "there have been significant interventions from the Prime Minister of Spain and the President of Catalonia, and it is not all clear what terms could in fact be agreed."