There have been efforts to
identify textures used in old 3D games like Mario 64 for a while now. Fairly recently I watched
this video about where a bunch of the graphics in Doom came from. It specifically mentions a series of photo CDs called "MediaClips" that were the source of some of the game's textures. Chrono Trigger was developed at a time where Square was just starting to dip their toes into the world of 3D rendered graphics (they even used some in Chrono Trigger itself) so I figured they'd probably have some of these types of CDs lying around for sourcing textures from. I've long thought that some of the backgrounds in CT looked like they may have originated as photographs, so I downloaded a few of these MediaClips CDs from archive.org and started poking around. I almost immediately got a hit.
This is photo "002" on the "MediaClips - Majestic Places" CD:
And this is the sky over Zenan Bridge:
They obviously touched it up by hand, but there's no doubt in my mind that this photo was used.
Encouraged, I kept poking around. There's this photo of the moon on the "Media Clips - World View" CD:
I checked it against the moon behind Magus's castle, but it wasn't a match. Later, for completely unrelated reasons, I was looking at the Radical Dreamers page on Spriters Resource and found this moon, which definitely
is a match:
Then I remembered that there's a moon in the Chrono Trigger endings where the characters float away holding balloons. It's hard to say for certain, but I think this might also be a match:
The moon photo on the CD is titled "APOLLO11A", so out of curiosity I googled "apollo 11 moon photos" to see if this exact image is common enough that it would pop right up in an image search. It did not, but while I was scrolling I found
this other one from Wikimedia:
The red circle is supposed to be pointing out the location of "Oceanus Procellarum" and is irrelevant here. The original photo without the circle was apparently taken by Wikimedia user Silvercat with a camera that came out in 2007, so this exact photo obviously wasn't used for Chrono Trigger, but there's definitely an extremely similar one out there somewhere that was used for the moon behind Magus's castle:
Kind of a bummer that it's not quite the right one, but I think it's pretty strong evidence that a photo was in fact used.
That's all I've found so far, but I believe there are more. Maybe not from MediaClips CDs specifically. There were lots of other stock photo CDs being sold back then. I think I just got really lucky with that Zenan Bridge sky. I'll keep looking though.