Will every ship in 3.17 have a physical fuel port on the top? And how will the second fuel port be used?

So no, not all ships will have the physical port on the top. That is part of the gold standard. So some ships that are coming are supposed to have it already, so it should be already planned for them. But the older ships, some of them need to have it added. So right now the Gladius already has it. And on the second part of the question, the second port is mainly there for hangar refueling. So the top one is just there for in-flight refueling with the Starfarer. And the bottom one is, if you're stationary, someone with a hose comes in and refuels your ship this way.