It's not just a position thing it's also a "type of strength" thing. Specifically the switching from eccentric to concentric.
I'll give you my own example. A few years ago when I first developed the layer system used lifts from pins exclusively in the program. I didn't use a progressive ROM approach though. For the bench press I started the bar from pins about 1" from my chest, so pretty much a full range of motion.
For about 3 or 4 months all my bench pressing was done from pins. I eventually worked up to 425 from pins starting the bar 1" from the chest,
I then decided to test my "real" bench press. I reasoned that since I was using pretty much the full ROM and that I didn't have the benefit of the stretch reflex, my "real" bench press would be at least equal to my bench from pins, likely more.
Well much to my dismay I actually failed 365... 60lbs less than my bench press from pins.
The problem is that both the eccentric and especially the turnaround from the eccentric to concentric were all over the place. Out of position and weak. And keep in mind that I've always been pretty decent on the bench press for many years prior to that.
Lifts from pins do have their place in a training, but if you train exclusively on them the transfer is indeed not direct or easy to "real" lifts.
The deadlift would be less negatively impacted and likely easier to transfer the gains to because in the deadlift there is no switching from eccentric to concentric as the lift starts from the concentric portion. But the issue with the deadlift is that it is easy to use faulty positions to cheat the way up on deadlifts, especially for pin pulls above the knees (people tend to "pry" their knees under the bar to leverage it up).
To be effective the progressive ROM technique needs to be done NOT from pins. You need to include both the eccentric and turnaround phase on each rep if you want the method to transfer to the "real" lifts.
This means lowering the lift as if you were doing the full movement but cutting your range short and switching to the concentric portion.
The problem is that it becomes hard to know where to lower the weight to. Especially if you have to gradually increase the range of motion over the weeks.
You could use the pins in the power rack as a target; lower the bar to the pins then press it up. The issue with that is if you touch the pins it changes the turnaround dynamic because part of the force you have to break then reverse is absorbed by the pins and the bar rebounds up a bit.
The only solution is to use the pins as a target and lower the bar until it's about half an inch from the pins then reverse the movement and press/squat/pull it up.
You lower the pins when you need to increase the range of motion.
But starting a lift from pins does not transfer well to real lift performance. It's purpose is when doing overload/partial work to strengthen the muscles and desensitize the Golgi Tendon Organs.... but it wont work well to improve full lift performance.
The only people I know who had a good carryover are those who also used similar lifts done "regularly" while training the main lift using the progressive ROM method. For example doing bench press from pins using the progressive ROM method and close-grip bench press with a normal method.