Obviously rape would have occurred, but not in large numbers otherwise it would have been documented.
These foreigners settled down, they didn't just screw the women and leave.
I'm not saying we are genetically more similar to them than say a non-Muslim Kashmiri, Punjabi or Sindhi, I'm saying we are descended from members of their societies who came during the Islamic conquests and our genetics clearly show this. However, they also show that these people did assimilate into the region and as a result form only a minor component of our ancestry (however, for some of us it's still fairly significant). Also, there were still plenty of people from Pakistan working side by side with them, occupying high positions (or forming their own dynasties) and being treated as equals, not as inferiors (a few crazies tried to peddle that theory but they flopped).
Pashtuns and Baluchis are genetically more similar to other Pakistanis than Baluchis or Pashtuns from Afghanistan or Iran.
Not always, we're all (mostly) pretty similar in colour and can be pretty fluid in terms of other parts of our phenotype, I have my fair share of incorrectly guessing someone's origins, and people have done the same with me.