When I use Arceus & Dialga & Palkia GX's "Altered Creation GX" attack do I take a Prize card if I Knock Out Lillie's Poke Doll?
No, you have to be able to take a prize card in order to take "an extra prize card".
Source: TPCi Rules Team (2019-11-14)

Relevant cards

Note: All applicable cards may not be listed below.
SM12_156
SM12_156
SM12_197
SM12_197
SM12_220
SM12_220
SM12_221
SM12_221
SM12_258
SM12_258
SM12_267
SM12_267