Mmmmh. First time I hear about this one.
I don't think it's true. Your story on Royal Road is not an ebook. It's not the same 'product'.
It is an ebook, it's just not compiled neatly as you would something you sell on Amazon. For the purpose of commercial use, whether it is neatly compiled or remain as a web novel, nobody in power cares. This argument that webnovel and light novel is not the same thing was used by translators in the past and it's not accepted by the court. By all intents and purposes, including legal, online literature is the same thing, no matter in what form it appears.
Therefore, if your Royal Road book bears the same title, plot, prose and story as the one you're selling on Amazon, it is treated as exactly the same thing. If it bears the same title and plot as the one you're selling on Amazon, it's considered a draft, and falls under the same rule as if it is the same thing. Basically, if it can be argued to tell the same story, it is the same thing, even if the book on RR has no volume specified. For that reason, it is well within Amazon's right by their Term of Use to make your book cheaper.
Regardless, Ai-chan too has never heard of Amazon making your books free if you put it up for free elsewhere. Ai-chan has made Felicia's Second Life webnovel version free for years. The argument here is not that it's a different product, it's that you specify that you allow Amazon to sell it, if they pay you for selling it. Bandwidth is not free and Amazon does not like to give handouts, so unless you specify it to be free, they won't make it free.