There is righteous scholarly discourse about this. A lot of it.
Evidence one: Once you know where to look for it, the signs of genetic manipulation are omnipresent. There are lots of non-coding segments with what was previously believed to be random junk in the Kitsune genome, and lots of other species' genomes too. But with evidence two, they can be sensibly translated. The Fibonacci sequence is encoded in quaternary in one of them! And a bunch of other first-contact-math type stuff!
Evidence two: There's literally a huge stone pyramid someone dug up a few years ago with a Rosetta Stone of an obscure stone age language to DNA. There was a Punnett Square on one of the walls. Archaeologically, the place seems to be about 10,000 years old.
Evidence three: Huh. By examining the rocks, it sure looks like the oxygen content shot WAY up and lots of fossils started appearing about 10,000 years ago. Funny, that. (They have a pretty basic seeming understanding of fossils. It sounds... Off.)
Evidence four: Everything on Iwami appears to be designed or bred to be pretty before anything else. There were theories at one point about runaway sexual selection but there's no reason for a tree to be pretty to Kitsune. Early biological scholarship was shortsighted and wrong about lots of stuff.
Evidence five: One of the gas giant's moons started getting all oxygenated after a probe visited it. There seems to be something growing on it. Sus. Did the Makers have other projects?
Evidence six: Translating the non-coding segments of genomes reveals a lot of what scans like prose or poetry. Most of it doesn't translate very elegantly but it seems like the Makers had a lot of religious and philosophical opinions, including on the power of the mind to overcome physical reality.
Evidence seven: Kitsune can alter the effects of particle physics experiments by thinking really hard in the vicinity of a particle accelerator. It's not electromagnetism or any other known force. It doesn't seem to matter what they're thinking about, but neural activity = tiny but measurable and replicable weird particle accelerator results! From Kitsunes, not from other animals, even! Those with more tails do it more strongly. Some people take this as evidence that psionics are just around the corner. The Academic Establishment is a lot more skeptical of that. Severed tails from people who donated their bodies to science also do it.
Overall things people mostly agree on is that something or someone made the Kitsune and also all other life on Iwami, they're long gone, they gave Iwami air and water and stuff in addition to life, they had strong religious beliefs that may or may not be true, they liked the number nine a lot (pyramid stuff is all in base nine and it comes up in the prose). Anything else is a fuckton of speculation and nothing solidly provable.