"In alternate shooting, the alternation between the teams will take place after every shot arrow."
To clear the doubt, this Article 7.6.5.2.3 is on SHOOT-OFFS only.
That means in the Finals when shooting alternate, a team still shoot 3 arrows (each member shoots 1 arrow) then alternation will take place for the other team to shoot 3 arrows. There is no change in the normal alternate shooting. It is only affecting the SHOOT-OFFs.