A better intercooler could help, but higher iat coming in I would think higher temps entering the throttle body, maybe i'm wrong.
The intercooler should take care of that. The air is going to be heated regardless when its compressed. If anything the temperature difference between the paxton and a p1 are more due to the head unit efficiency than anything else. I have not tested this but I'm willing to bet that the its temps are going to be very very close to each other asuming that we run the same head unit and intercooler. At idle the its might be a bit higher but once the car starts to move it should be the same. The if the intercooler is large enough like a paxton kit at base boost is not even close to being maxed out. There is more than enough surface area to reject the extra heat from where ever the blower is sucking air from. I just hate seeing people use the intake placement of the procharger as a reason not to buy it. I think it just sounds silly.