It's a fantasy setting because it has stuff like the daelkyr and the dragonmarks and the Church of the Silver Flame. If your characters are dealing with those mystical elements, you're doing fantasy. But if your adventure revolves around an engineering problem aboard the lightning rail or some other consequence of industrialized magical technology, then yeah, you're veering hard into the realm of science fiction.
Me too!
You sure about that?
Completely sure, at least in case of arcane magic. Even divine and nature magic is, at most, mysterious in terms of where it comes from. How it works is predictable. Arcane magic is straight up scientific.
Eberron is a fantasy setting, and would be regardless of the elements you list. The Silver Flame isn't even especially mysterious. Heck, divine magic comes from faith, and most clergy and such know that. Again, mysterious to commoners perhaps, but not to the people using it.
The lightning rail is a fantasy world element. It isn't sci fi, at all. Warforged and airships, either. They are all powered and/or created by magic, in a fantastical world that runs on magic. That is fantasy.
A world where the street lights are powered by a magic ritual, ships fly through the air because magically boyant wood and bound elementals, and there are beings made of living wood and stone who think and feel and can access divine (faith based) magics just as well as any human, and thus very well might have souls, is a fantasy world.
or perhaps you think Harry Potter isn't fantasy? Magic is understood, studied in school, predictable, and permeates every part of life, from flying buses to healing potions.
A fantasy world is fantasy because because it is fantastical, not because magic is mysterious and can't be understood.
An adventure set on the Lightning Rail, dealing with the system that moves the thing forward, would absolutely be fantasy. It's a magical floating train! I don't remember for sure, but the forward momentum probably either comes from a bound elemental, or the same magic that makes the thing float.