I'll preface this by stating that I'm not a QC or anything, simply an interested party. (There is a niche area of trading currency/stock which relies on understanding and unpicking cases/appeal cases. For example, a stock could crash because a company loses a case on their items safety, but the appeal could give a different outcome.)
From what I understand, NO court accepts the absolute authority or sovereignity of Parliament. I think this was most strongly alluded to in Jackson et al vs Attorney General in 2005 (House of Lords/Supreme court)
https://en.wikipedia.org/wiki/R_(Jackson)_v_Attorney_General This case is very important in this instance, as it's really the first since 1929 or so in which the Judiciary really assault the domain of the executive. It's also significant in that they found it justiciable. (Funnily enough, during this case they also gave the example of Scottish Law set out in the 1707 act as something Parliament couldn't just ramrod.)
So tl;dr:
No court in Either England or Scotland accepts that parliament is absolutely sovereign.
The main issue that has been fought so far is: Is this case justiciable; that is to say, do the court have the power to decide or is it a political problem?
The High Court and Outer Court of Session decided it is not so - whereas the Inner Court of Session surprised us and decided it is so. The bar for the judiciary to get involved is pretty high; the government have a lot of leeway before they will go for this. Both in Scottish and English law. (Assume the law is the same, it's pretty much so). This is why the Inner Courts decision surprised us. It's also the major barrier to a decision against the government in the Supreme Court.
I think the difference in the decision was simply due to the seniority of the judges. The CoS ones decided they wanted to get it on record prior to the Supreme Court ruling, whereas the High Court took the 'safe' route and just passed it upwards.
Ps. Yesterday I said 'flip a coin.' I'm personally starting to lean ever so slightly to a verdict against the government. I think. Whether this is personal bias or not is another matter.