Shalom, This discussion in the Gemara (Mitzvot Tzrichot Kavana) appears to be somewhat superfluous and this is why: The Mishna says – Sof ma’aseh machshava techila – the end of a deed/action is a thought first. This is a basic human function which happens automatically by defualt, so why discuss the issue of kavana (intention) at all? Example: If you wish to drive a car you must have the intention to drive a car, it happens automatically, otherwise it is impossible to do it, so why discuss the issue of kavanah? It happens automatically! Can you please answer this question?
The Talmud deals with how to view the many different levels of kavana (intentions). There is the basic kavana that I'm doing a mitzva or Godly act, e.g. when one does a favor for a friend, he may not necessarily think of it as a mitzva, or if one is born if the Land of Israel- he very well may not realize he is doing a mitzva every second! Also, if one has kavana to say the Shema prayer, but doesn't focus on the words he says, he has one type of kavana but is totally missing a different type of kavana. There are those who succeed in concentrating the kabbalistic ideas each and every time they pick up the lulav and etrog, which is another totally different type of kavana [By the way, your quote is not from the mishna but from the Lecha Dodi prayer.] All the best!