I have a 95 chev shortbox. I had a gsp 16000 5th wheel installed in my truck. I haul a 22 foot 5th wheel with a extended pin. The company that installed the hitch put it 3 inches ahead of the axel. I was turning around my 5th wheel when it went through the back window. My question is: Was that the proper place to put the hitch in a short box?

I would have to say no, that was not the proper place for the clearance of the back window but was the proper place for weight ratings and handling.
I have done it myself with other things that have been set up by others and never checked the install without driving off.
You might have to get an extended pin box to regain the camper to window clearance and still retain the handling of the truck.

It is the correct place for the hitch. No matter Bed length you want the hitch forward of the axle. more forward it is better the ride and weight distibution is. I was in the Rodeo and Horse biz all my life and have had many truck installed with goose neck balls and fifth wheels. Just have to be careful with a short box truck. The spec I was always told by a very reliable installer in Indy was 4-6 ahead of axle.

We have a pull rite hitch. I will not have any other type. It will automatically move to the back when turning sharp. Check them out before buying anything else....Doc

You need a slider hitch with a short box pickup. 3-4" ahead of the axle is the correct.