In the email extensions in Mfiles.VAF.Extension there’s an option for UseEncryptedConnection and I assume this relates to the “Use encrypted connection (SSL/TLS)” option under Notification Settings. Question: Is this compatible with TLS 1.2?
I believe you already got an answer from Craig via other channels, but for others following this discussion: TLS 1.2 support should be a combination of the support on the OS level and the dotnet runtime version. If you are targeting .NET 4.5 then there's a line of code needed to enable TLS 1.2 (Stack Overflow). If targeting .NET 4.6.2 upwards it should be enabled by default.
If it doesn't work then you should raise an issue on the VAF Extensions repository and, if you can, submit a pull request with a fix.