I replayed that part of the story using some old save states and reviewed a map of SF2's overworld which led me to the same conclusion as you:
Battle 12 is definitely the same location as Sheela's Dojo and Battle 13 is not only visually similar but also confirmed through the dialogue to be the path to Roft. Although Battle 16 is far more dry and sandy than the Prism Flower battle, it is right before the Dwarven Town story-wise and the layout is exactly the same. The stronghold was said to have been built to keep the monsters from spreading too far, so it would've been massive making that stretch of land an ideal choke-point.
Although there is nothing in SF2 to suggest the presence of a fortress there either visually or through dialogue, there is no place Eiku's Fortress could've possibly been except for the stretch of land between those two mountain ranges.
Not that it matters, but here's the SF2 Overworld Map I referenced when researching this:http://www.vgmaps.com/Atlas/Genesis/ShiningForceII-World.png