This is because these are British dependencies or have a special relationship with the UK but at the same time are independent.
(IANAL, this is my lay understanding and is provided for entertainment only and should not be taken as legal advice, etc:)
Legal tender means you cannot claim a debt remains unpaid if you were offered repayment in the form of legal tender. So if I owe you £1000, you could in principle refuse to accept Scottish notes if you chose to and maintain that the debt stands (although that would be pretty crap of you, and you must accept the English notes after I've changed them at the bank).
Retailers are allowed to accept pebbles in exchange for goods if they want, and would normally accept Scottish notes on this same basis (they want your business). I believe they could even refuse to accept legal tender: a retail transaction is considered to be making a contract rather than repaying a debt and therefore has little to do with legal tender (see also: 'invitation to treat').
I also suggest that retailers in London accept Scottish notes almost without exception.
[0]https://en.wikipedia.org/wiki/Legal_tender#United_Kingdom