The thig is, this still is overcomplicating things for her origin. I mean, Kanako changing can actually be easily explained by how flexible gods are; going by SoPM, gods are shaped by their legends and myths, so if, say, a group of people started to think of Take-minakata as a female deity of the wind, he's eventually start to appear as that to them. Gods can appear in whatever form they want (Suwako is said to take the form of frogs when called on different shrines, for instance). They can't really be used as an example in this case.
See, Miko has full memories of the time she was emperor; furthermore, no one that was alive in the time she was supposed to have ruled (Futo, Tojiko, Siga... Kanako herself existed back then, and would've certainly heard of Miko) question her apperance or her existence as a ruler. If she was a fully fictional charater given life inside Gensoukyo because of the controversy over her existence, wouldn't at least Kanako note that?
Also, the profile clearly states that the mausoleum was moved to Gensoukyo, because of its nature of attracting things thought to be legends or that are fogotten. Look at this passage from the profile:
"Because Buddhist monks continued to place seals on Miko's mausoleum, she was unable to resurrect. Miko's plan had been foiled.
Miko judged she had no need to rush and could resurrect herself at any time, and so continued sleeping. Finally, the time of her resurrection came.
The trigger was a rumor that the legends regarding her were all fabricated. Since, in modern times, there were no more people with superhuman powers, it wasn't surprising that tales of her exploits were seen as simple lies.
As a result, her mausoleum ended up in Gensokyo. Since there weren't any temples in Gensokyo at that time, she prepared for her resurrection to proceed whenever she felt it was necessary.
By some stoke of timing, though, a new temple was built.
And, whether by plan or by chance, it was built directly over her mausoleum.
That was, of course, Myouren Temple."
In other words, the only reason she didn't come back to life in the outside world was because people kept putting new seals on her mausoleum. Maybe, if people continued to believe she wa real, and someone finally stopped sealing her, she'd have come back to life just fine in the outside world. I mean, magic's not entirely dead there (Maribel, Renko... heck, Mamizou lived there until recently).
tl;dr, I still think applying Occam's Razor is the safest bet here; she was always a real, female ruler of Japan, and her gender was simply lost to time. The reason people thought she was a legend is clearly stated in her profile ("(...) a rumor that the legends regarding her were all fabricated. Since, in modern times, there were no more people with superhuman powers, it wasn't surprising that tales of her exploits were seen as simple lies"). It seems more palpable considering what we have in terms of canon info than saying she's a construct that suddenly spawed in Gensoukyo because of people debating Shoutoku's existence. Well, at least I think so, anyway.
