Having looked into this, I would say that it's something that's not actually been tested in the courts yet as the wording of the law is unclear. Is it the value of the share in the first property, or the value of the whole property? How brave do you feel like being with the courts?
My reading, and I would strongly suspect the courts would see it the same way given the intention of the law, is that you would be liable for the extra SDLT as the first property is worth more than £40K. That would make sense, and this guy appears to agree with me. That said, I would simply speak to the solicitor you would be using and ask them: If they say yes then fine, and if they say no then you can simply sue them for the amount if they're wrong.