All those things are true I just find myself resisting the illustrations that it means the leading and conviction of the Spirit - rather it is He Himself who has baptized us into the body of Christ.I am not sure what you mean by "molecular" but the usage of the terminology of "by one Spirit" is similar to:
Luke 2:27 And he came by the Spirit into the temple.
Did the Spirit pick Him up and carry Him or did it lead Him to go into the temple?
Luke 4:1 And Jesus . . . was led by the Spirit into the wilderness.
Taken by the hand and pulled along, or influenced and encouraged?
I know that I followed the Lord in believer's baptism due to the leading/convicting of the Holy Spirit in my life. And doing so made me one with the body, in unity with the local assembly belonging to the Lord.
1 Corinthians 12:13 For by one Spirit are we all baptized into one body, whether we be Jews or Gentiles, whether we be bond or free; and have been all made to drink into one Spirit.
There is the metaphorical statement at the end of the verse "all made to drink into one Spirit" don't know of any churches which requires candidates to drink the water
HankD