Owning a Prestige Edition skin should entitle you to the "Variation" discount.

For example, let's say someone owns the Prestige Akali skin. They're a huge Akali fan, and want to have a perfect collection of all her stuff (like I do with Sona and Zoe). They already earned one version of the skin, so there's no reason they should still have to pay full price just to get a lesser version. They should use the same logic as with Pajama Guardians and Eclipse Leona, and reduce the cost for players who already own the prestige edition by 45%.

Ideally it would just come for free when you get the prestige edition, but Riot needs to make money and I feel this is a fair compromise.