The bolded portion of your statement is incorrect. There are demonstrable examples of Institute Scientists going to the surface or having grown up on the surface.
Dr. Madison Li
Dr. TS Wallace
Dr. Enrico Thompson
The latter two are both in the mission "Pinned", where Enrico refers to being up above as 'field work' and implies that other scientists have also been to the surface because he's complaining about how they should have sent someone else that was more qualified for doing it. Dr. Li is very prominently previously seen in the Capital Wasteland during the events of Fallout 3 and works with James, the Lone Wanderer's father repeatedly. That she was first seen in the Capital Wasteland later in the Commonwealth displays that she's quite well traveled for a Wastelander.
At the beginning of FO4 she starts as the Division Head of Advanced Systems (and remains so unless convinced to leave - admitting that she's growing disillusioned and uncomfortable with the Institute's and Father's directives). So... one of the Institute Division Chiefs was not born within its walls, is well traveled, and has worked with the Brotherhood of Steel and other unaffiliated scientists in the past, one of whom -- James -- is noted for his adherence to strict ethics.
They most certainly have experienced other points of view.
I believe you need to reconstruct your argument.