It is his father yes, but it sounds like he has already spoken with him several times about it and his father won't stop. In situations like this, you have to be a bit of a hardass. The only way to stop him is to physically prevent him from entering the house, via a lock that he can't open. Yes, it is difficult when it's your own father you have to lock out, but the father has shown that this is the only thing that will stop him from being so invasive, so the roommate has to find the stones to do it.

It also sounds like the father could use some...er...professional help, but no one can make him go. The roomate could suggest it possibly, although that can be very difficult to do diplomatically, but he can't force him to go, so he needs to take measures to protect his privacy himself.

If not, then the father is going to keep cleaning his room every day, and there's nothing you can do about it, so don't make it your problem. Take steps to protect your own living space/stuff and don't worry about it