Lunar Threads

Lunar sega cd was very mystical had staves , and was a medieval world filled with wizards demons and magic books
remakes in the blue star was a futuristic world full of technology when it was destroyed Althena with his spaceship turned into a habitable world contained energy on the ship that really she had no magic
lunar ssh has a futuristic scenarios pentagrams become in technologic orbs, althena tower is a spaceship, etc etc
I personally prefer the medieval and magic touch of the first version

Except...The Grindery was powered by a Steam Engine (technology) on SEGA CD, but in the Remakes it's power came from by Dragon Energy (magic, or even Magitek if any of you are familiar with FF6.)

I only played the PSX versions of the games, but if I'm not mistaken, it's never said that Althena didn't have magical powers, she just transported them with spaceships. Many "real" deities got special vehicles to (Apollon's chariot, or Kubera's Pushpaka) and then left one or humanity to return to the Blue Star without her help, to her that was apparently mainly a back-up thing, but there're a lot of "real" gods who helped humans like that in the myths (i.e. by teaching them agriculture).

Many RPGs feature "magic" as a form of powersource, Shinto-Cetra already named FF VI's MagiTek, other examples I could think of would be FF IX's mist engines for airships, Star Ocean's heraldry/symbology, Xenosaga's ethers, or Phantasy Star's photons - and then there're FF VII's mako energy reactors which are essentially nuclear power plants. I really don't think these two cancel each other out. Even our modern day technology could be considered magic: right now I'm writing without writing on an immaterial paper sheet, so that somebody thousands of kilometers away can read it. A few hundred years ago I would have burnt on the stake for such sorcery!

Personally, when I think of a science fiction game I would always expect ESP/PSY-energy to be a thing, just as I consider it a given that a fantasy game's story is related to a highly advanced civilisation...why at least in a japanese production. They really go hand in hand.