Every hole in that roof is a potential leak. That is why you rarely see equipment on the roof. Penetrations to the building are almost always on the sides, hence the mechanical court yards.
One of the factories I worked for regrets the decisions they made 50 years ago to put most of their utilities on their rooftop but not for the reason you point out.
Every hole is a POTENTIAL leak but what I have seen it is almost never a problem.
Holes are made for pipes transporting heat/cold/product and for cable ducts but are always constructed so that the in/outlet is under a utility device and is higher than the edge of the roof so that if the roof gets flooded the water spills over the edge of the roof, and are also water tight.
The main problem causing damage to a roof is PEOPLE working on the roof.
They might leave rubbish on the roof, like shards of metal, ty-rap/Cable ties, bolts/nuts/screws which can lead to holes in the roof surfacing when you walk over them.
This is by FAR the most common cause of leaks on the roof of this particular American Chocolate Company.
Also, those ty-rap/cable ties to bundle electric cables disintegrate due to UV(10-20 years), fall on the ground and cause trouble when people walk over them.
People should also always try to stay on the rubber thicker mats tracks but rarely do if there is a short cut, most just don't realize the roofs sensitivity to people walking over it.
Edit: workers dropping tools/gear or any heavy materials is also a problem.