If one accepts the principle that allows Scottish independence / devolution, the principle applies to smaller units. This is why Norn Iron exists.
The SNP have already accepted that the Northern Isles are a special case that should have power devolved to them. The law in the Northern Isles differs (slightly) from Scotland. Historically the Northern Isles were Norwegian and there was no consultation with the islanders about the transfer to Scotland. The Northern Isles are clearly politically different from Scotland in the same way as Scotland is from England. See the general election and referendum results for how the Northern Isles differ from Scotland. There is no recognition of language rights for the Northern Isles - the Western isles get a huge hidden subsidy through gaelic language support. Small nations / crown dependencies do exist. Out of the EU the Northern Isles would be financially viable, especially if Scotland was in the EU (trips to Orkney would allow the purchase of duty free goods). It is only not an option because the Northern isles would take a lot of the oil, gas and fishing, impacting on the financial viability of Scotland.
The principle of independence from the United Kingdom applies to the constituent countries of the United Kingdom, and not to smaller geographical areas. In the event of our gaining independence, it would be the height of arrogance for any future Scottish government to instruct the rump UK administration on how the affairs of Yorkshire, Gwent or Cornwall should be dealt with.
As I pointed out in #425, this is simply Unionist mischief making. The unionists don't give a toss about the particularities of the N Islands, as the UK has had centuries to deal with this, if any remedial action were required, and has done nothing. Any matter connected with those islands, or with any other part of this country, will be managed by an independent Scotland if and when it comes into being.
The partition of countries, including Ireland, that have had the impertinence to secede from the British Empire, is an old, tried and trusted imperial tactic. We're used to it. It is one of the things people expect in these processes. We are neither surprised not frightened by it.
By the way, the threat of territorial mutilation by amputation of the oil-rich N Islands conflicts with another Unionist scare tactic, which is to frighten people here with the notion that oil and gas are now permanently worthless, rendering independence financially impossible until the end of time.