Yes as long as you have one PPP unlock you can pick whatever PPP you want for your second build, and it will only affect that build. So you can have Mako on one build and Ghost Widow for your other build.
"All right, they're on our left, they're on our right, they're in front of us, they're behind us...they can't get away this time"- Chesty Puller US Marine Corps
Awesome!
So let's say you have a lvl 50 villain and you have Mako for your PPP. You create a second build and decide to go to another PPP. Can you do it and will it only affect the one build or both builds?