Hmm... you know, a simple accident that backfired and had an effect on tanuki genders - likely a plague medicine that worked, but had drastic side effects - would be okay with me. Like you said, same idea of magical abuse/risk, but no nasty political implications.
If that's the case, we'd need to figure out what effect it actually had.
For comparison, in Tainted Space, the "Kui-tan" (sci-fi tanuki) were afflicted by the Kintama Plague; a male virility booster gene-mod that went viral and infected the species, causing not only males to develop mutated testes that visibly inflate with semen due to heightened production, but for females to grow functioning (and similarly afflicted) male genitalia of their own.... I did warn you it was NSFW.
Ah, I see. Yeah, that makes sense, and you're right, it's easier and better lore to have it that whatever connection - if there is any connection, it might just be rumor, hearsay and speculation - is something that only the top of the top would know.