Say Zoroark GX has Unit Energy {F}{D}{Y} and Rainbow energy attached and uses its "Trickster GX" attack to copy Arceus & Dialga & Palkia GX's "Altered Creation GX" attack. Can Zoroark GX use the extra effect of +1 prize for every KO from Altered Creation GX?

Nope, the two energy attached to Zoroark GX are used to pay for the Trickster GX attack (regardless of how much energy is required for the attack being copied), so in this case there is no "extra Water Energy" to permit the extra +1 prize effect.

Relevant cards

SM12_156

SM12_220

SM12_221

SM12_258

SM35_77A