That doesn't happen in Zou and Punk Hazard as well. Water 7 had nothing to do with fighting CP9 agents. The straw hats came into Water 7 to repair their ships not rescue Robin and fight CP9 agents. Water 7 was set up for Ennies just like how Punk Hazard, Zou and Dressrosa were set up for Wano.
The main conflict in Zou was figuring out the mystery of what happened there and taking care of Jack. Both those things are resolved. The main conflict in Punk Hazard was defeating Caesar and saving the kids.
The main conflict in Water 7 was
- Usopp and Luffy having a falling out due to the Merry
- The attempted murder of Iceberg
- Robin seemingly leaving the crew
None of these plotlines get resolved in Water 7.
Zou starts immediately after Dressrosa and Dressrosa starts immediately after Punk Hazard so I don't understand your point? Same logic can be applied.
Zou starts roughly a week after Dressrosa iirc, and Dressrosa starts a few days after Punk Hazard. Enies Lobby starts a few HOURS after Water 7. Again, that'd be like if you considered Onigashima and Wano different arcs
Also, Water 7 and Ennies Lobby are different arcs not because they take place in different islands is because they both have different settings, different themes, different story lines, etc. The only aspect that carries over are the characters. The characters don't change.
The main theme of Water 7 and Enies Lobby is that every friend is irreplaceable. They do not have different themes.