I just double checked, and they don't even say Mercphobia lifted an ocean. They said he lifted a sea, which is much smaller than an ocean. For example, the East China Sea is the Atlantic Ocean, and doesn't cover anywhere near the entire span of the Atlantic. Mercphobia probably just lifted some of the water near the coast of Elimina, not all the water in the ocean between Giltena, Ishgar, and Alaktasia. Also, Natsu thought he was going to kill Mercphobia with his secret art and that was after he saw Mercphobia lift the ocean.
Ignia's flames were never meant to vaporize the water. He wasn't attacking Mercphobia. In fact, he made a strict point that he wasn't going to personally fight Mercphobia. Ignia just wanted Natsu to eat those flames. Ignia just used an attack on the city to make some flames, and probably even held back on the attack because we know at full power Ignia can destroy a country. Mercphobia then tried to put out the flames by dropping the sea on it. So Ignia's attack didn't destroy Elmina, and Mercphobia's attack also didn't destroy Elmina. How can both be multi-continental? These are very both clearly city level feats.
You can't lift and drop a continent's worth of water, or vaporize a continent's worth of water, without effecting the ecosystem. Continental level feats should involve mass changes to...well, a continent. If it's contained within a city, well then it's simply not continental. Etherion would mess up the ecosystem if Tower of Heaven didn't absorb it. Remember Hiro Mashima's previous work, rave master? When Etherion went out of control there, it blew up 1/7th of the landmass in that world. In Fairy Tail, it's dailed back, but it still said to be capable of destroying one of the countries in Ishgal.
But again, how much water Mercphobia lifted isn't important. Natsu was actually swimming through the water in the sky. The water itself doesn't do any damage. It's only dangerous when Mercphobia uses a whirlpool to suck you in and drown you. We have feats of Ignia swimming right through Mercphobia's whirlpool. Igneel has enough physical strength to brawl with Acnologia for 20 minutes. They were both cut up and bloodied after that fight. Igneel should be able to give Ignia the same trouble if the two ever brawled, so that's more than enough physical prowess to swim through Mercphobia's whirlpool. As far as Mercphobia's other attacks goes, the water pillars and his roar would all be fairly easy to tank. If you accept Mirajane's filler feats as canon, which I believe you do, then Igneel has feats of his punches matching Acnologia's roars. That's more than enough to suggest he can tank Mercphobia's attacks.