I assume the rule at page 16 quote above means that you can't build a new mine/mine shaft that cumulates the effect of specialization to populate the mine with 12 iron and 8 gold / 8 gold and 9 iron. That is, when a player has researched both mine technology advances and they come to build a new mine/shaft they add to the mine bag:
3 iron AND 3 gold (basic); OR
4 iron OR 4 gold (specialized); OR
5 iron AND 5 gold (big).
This is correct (I corrected your big mine typo). You designate what kind of mine you're making at the time that you put chits in the plastic bag. Every time you put chits in the plastic bag, it is your option as to which type of mine to choose, from among those you've researched.