Since we're dealing with coats of arms, we have to take a (or an, if you're British) [[[heraldry|heraldic]] point of view; and by it, Mais Oui is perfectly right. Every heraldic manual I've ever seen has referred to the arms Astrotrain keeps adding as something along the lines of "the royal arms for Scotland" or even "the royal arms as used for Scotland." It is perfectly clear that they are actually the exact same coat of arms as the ones to be found at Royal Coat of Arms of the United Kingdom. 

 "How can that be?" you ask, "those arms are visibly different." The answer is that they are different versions of the same arms. Let me give you an example. Supposing that my father has a coat of arms and so does my mother (either she was granted it in her own right or she has no brothers to pop in before her). I then inherit both of their arms on their deaths. Now I can easy quarter their arms (in the same way that England, Scotland, and Ireland are quartered on the UK arms); but what do I do with the fact that they each had a crest sitting up on top? (Well, unless she's really modern, my mother didn't use hers; but her father did.) Some people, in displaying their arms, include multiple crests (if they are entitled to multiple crests) in displaying their arms. Others thing this look silly and just choose one. Let's say that I like my mother's crest better and choose it. Then I die; and my son prefers my father's old crest. Is it available for him to use? Yes! Just because I didn't use it doesn't mean it didn't exist; it was still there, invisibly. Likewise with my parents' supporters (if they were so lucky as to have these rare honors). Say my dad's are an aardvark and a beaver while my mother's are a yak and a zebra. I'm free to choose any two I want; and if I use the aardvark and the yak, my son is free to choose the beaver & zebra instead if he prefers. The point of all this: a person's arms include all those symbols to which he/she is heraldically entitled; the visual display of them is entirely up to that person. The queen has one coat of arms, which she chooses to display differently in Scotland than she does elsewhere; in Scotland the Scottish elements have pride of place. 

 Until devolution, it's clear why the Scottish Office in Westminster used the queen's arms for Scotland: they are a ministry of her UK government. Now I admit that their use by the new Scottish parliament is a little confusing; if they're a national Scottish institution, what are they doing with English and Irish symbols on their arms? Well, first, it's not their arms — it's the queen's, which they're using by permission and as her delegates. And secondly, I'd guess that the possibility of using the plain lion rampant, if it even occurred to them at all, was rejected because it could be interpreted as a sign of Scottish independence. 

 Could it be so interpreted here? No, we're not an official government institution displaying it as our symbol; we're reporting in the third person on somebody else's symbol. A country is more than its government; and so while the lion rampant is obviously not used by the Scottish parliament, it is a national symbol of Scotland. And, in fact, to a herald, it is Scotland. It is absolutely & 100% analogous to the three lions in England — the old royal arms of the kingdom, now never used because the kingdom has acceeded to a United Kingdom.  |