TheBBC reports that Westminster is claiming a Scottish independence referendum wouldn't be able to use the full electoral roll, which seems a bit strange:
Scotland Office Minister David Mundell said: "The UK government has set out very clearly that the Scottish government cannot legislate lawfully for a referendum with its current powers.
"The full electoral register can only be used for specific purposes such as the general or Holyrood elections.
"The legal position is clear - if the SNP attempts to go ahead with its own referendum then it will be nothing more than an opinion poll, with a million Scots unable to be asked for their view."
If true this means many potential voters could be excluded as they're not on the publicly available (reduced) register. As a layman I've had a quick skim of some of the acts related to the electoral register and according to the explanatory note of the Representation of the People (Scotland) (Amendment) Regulations 2002:
A copy of the full version of the register may not be supplied by a registration officer otherwise than in accordance with an enactment (which, by virtue of the definition in inserted regulation 92(2), includes subordinate legislation) including the principal Regulations (inserted regulation 94(3)).
The effect of which includes an enactment to be 'any provision of, or of any instrument made under, an Act of the Scottish Parliament' via the Representation of the People Act 2000. Which, again I might be misreading, I take to mean the Scottish Parliament can in principle have referenda using the electoral roll. If they can use it for even a non-binding question about a reserved power is contested.
As Matt Qvortrup sort of arguesin the Scotsman, the international recognition of self-determination (which I think is less strong than he suggests, but going with it) would likely mean in the event that Scotland holds a democratically legitimate but illegal referendum, it would likely have to be recognised by Westminster - which is why moves to de-legitimize the potential vote by arguing people will be excluded make sense, and as I've said before the SNP should be careful to avoid ambiguous questions that give rise to these kinds of challenges.
Update: Ah, clearer copy of SNP statement that seems to support my point.
However a spokesperson for the Scottish government rejected Mr Mundell's and noted that the referendum would be carried out after the appropriate legislation was passed at Holyrood, ensuring full access to the register.