First of all, ligament gains can and often does translate into non-bone pressed gains simply by allowing the penis to reach futher out from the pelvis area.
I understand your way of thinking and I've asked myself this question many times.
There are more than one theory on the subject. I think one should separate ligaments gains from what you call shaft gains/growth (I believe this is usually refered to as tunica gains).
True, ligaments gains do not affect the actual penis size (shaft) but helps to reposition the penis so that it looks bigger (which is great btw).
Now, I believe the consesus is that the type of gains that enlarges the actual penis/shaft is caused by enlarging the main limiting tissue, namely the tunica, thus the name "tunica gains".
There are more than one theory about how tunica gains work as well. I personally think the "elasticity theory" (dont know if I'm allowed to link to the thread on thundersplace) is the most plausible one at the moment.
My understanding of the theory is that the elastic properties is lessened, through PE, to allow the tunica to fully expand to its true potential. This basically means the tunica doesnt get bigger BUT the effect is that more blood can enter the penis since the tunica can expand more. So the end result is that when erect you are bigger but you didnt technically "enlarge" anything. This also means that the tunica gains is ultimately finite and will be harder and harder to achieve.
Think of girth gains, for example, they are not caused by ligament gains surely?