My pin squat in weightlifting shoe is just above parallel, which happens to be right at my sticking point. I might be able to lower the pins just below parallel if I take off my weightlifting shoes. Should I?
It doesn’t matter at all. If you push your knees further forward you’ll be below parallel, regardless of footwear.
Sorry, English is not my first language. What I meant was that the pin settings are set to far away from each others.
This means that I am not able to hit the pins (without relaxing) when they are located below parallel. Since it is recommended that the pins are located below parallel, the only way I am able to do this is to either stand on something or take off my weightlifting shoes.
So am I better off squatting with shoes with the pin just above parallel, or without shoes with the pins just below parallel?
No I understood 
My answer is the same- it doesn’t matter. If you are >1" above parallel, I’d stand on something. If you are <1" above, I’d just push your knees further forward to achieve depth.