Thanks for your reply, @AGoodman. Logic would dictate that a mortgage would have no bearing on the SDLT, but from my research online, (including HMRC's own information), a mortgage does, for no good reason, seem to have be relevant (unless I've got this all wrong):
From a random website (https://www.quittance.co.uk/conveyancing/advice/transfer-of-equity/do-i-pay-stamp-duty-land-tax-sdlt-on-a-transfer-of-equity):
David owns a property worth £600,000 and is mortgage-free.
David and Sheila get married and David gives 50% ownership of the property to Sheila. As there is no mortgage, there is no 'chargeable consideration' and therefore no SDLT is payable.
However, if in the above example, David has an outstanding mortgage of £400,000, Sheila will have to pay Stamp Duty on £200,000 (£400,000/2 = £200,000) - this being the 'Chargeable Consideration')
Stamp Duty is only payable on the mortgaged part of the property. If the property is wholly owned then no Stamp Duty is payable.
From HMRC (https://www.gov.uk/guidance/sdlt-transferring-ownership-of-land-or-property):
Example 2 – you pay SDLT even though no money changes hands
The owner of a property valued at £500,000 with an outstanding mortgage of £400,000 transfers half the property to their partner when they marry in March 2020. Their partner takes on 50% of the mortgage (£200,000).
HMRC charge SDLT on the amount paid for a property or the amount of ‘consideration’ given.
By taking liability for the mortgage, the owner’s partner has given ‘consideration’ of £200,000 for their share of the property which is £1,500 SDLT (0% of £125,000 + 2% of £75,000).
They must pay SDLT on that amount and tell HMRC about the transfer by filling in an SDLT return.
The equity is not included in the calculation as you only pay SDLT on the consideration given.
...and from https://www.moneyhelper.org.uk/en/homes/buying-a-home/stamp-duty-land-tax-transfer-ownership-land-property-england-northern-ireland :
The owner of a property worth £500,000, with an outstanding mortgage of £400,000, gets married.
They transfer half of the property to their partner, who takes on responsibility for half of the mortgage.
The person receiving the transfer has a chargeable consideration of £200,000, which is over the SDLT threshold.
The new owner will have an SDLT liability of £1,500 (0% of £125,000 and 2% of £75,000).
Seems like a lot of nonsense, right?!