Depending on the bond location the atoms get passed through with 0, 1 or 2 P delay, but always in the order such that the atom with two bonds is passed through second (and the other two first and last respectively).
The right side assembles the molecule (this is easy given the same order always), and then rotates it for 2, 1, 0 P to get the correct rotation.
This works with synced arms doing grab rotate drop because 0/1/2 and 2/1/0 match up
in short, trit encoding in period delay