I'm planning on infusing some sandwich panels that will be 1 outer skin of 200gsm carbon 5mm perforated PVC core and 1 inner skin of 200gsm carbon. Will it negatively influence my infusion if I only put peelply on the inner skin (bag side) where I plan on doing secondary bonding? The whole thing would have a layer of P3 film and flow medium on top of it.

No not at all, it's totally fine.