When you transfer chargeable securities there are two charges arising: first, a charge to SDRT; and secondly a charge to stamp duty. The charge to SDRT is franked by the payment of stamp duty. The stamp duty charge is eliminated by a claim to relief from duty under s77, FA 1986.
So do you have an interaction of SDRT with stamp duty? ... yep. Stamp duty has to be paid within 30 days. So in theory you need to make the claim within 30 days to get rid of the duty and frank the SDRT. There may be interest and penalties for late submission but generally a successful claim to s77 will clear everything up. And SDRT does have a six year period.
You're right. Section 251 says no gain on the disposal by original creditor unless it's a debt on a security. If it's not the original creditor then there is a gain as it is an asset. Only exception would be where you're acquiring on trading account.
But I think you knew that :)