The coloured dots are normally just paint spots on the tyre.
Re the tread variation, it isn't uncommon for a manufacturer to have a few marginally different varieties of a tread pattern. They are normally varied to meet the requirments of different vehicle manufacturers, in accordance with their NVH (Noise, Vibration, Harshness) testing on different suspensions.
In your case I'd say one slipped through the quality control which was meant for some other car manufacturer who also uses them as OE.
They may have been made in different Hankook factories.
Each tyre has a serial number on it which will include a date of manufacture. These 4 numbers are normally at the end of the serial number - such as 2509 which would tell you the tyre was manufactured during the 25th week of 2009.
Before those four digits will be a sequence of letters. Mine say T7DH EK H. Those will tell people at Hankook where the tyre was made and a bit more info besides. If your spare has different letters on it to the four on the road then it will have come from a different factory. If they are the same then it came from the same factory but if that's the case one would assume the date would vary.