The geometry of the blade and spring junctions is somewhat complex.
When the blade is open, the spring pushes on the very inner end or corner of the tang while the back square in turn pushes against the end of the spring, all to keep the blade snugly open. These tensions also give you the "snap" we like to hear.
In the closed position, the spring pushes on two points of the tang, the inner end or point of the tang (the opposite side of when it is open), and the kick.
If you file the kick, you lower one of the two points, and the spring moves inward slightly. The only way to raise the spring back is to disassemble the knife, and forge the tang corner out, to push back on the spring, raising it again. This is a time consuming, and delicate operation, only achievable by the best cutlers.
The parts of a production knife are mostly NOT CNC'ed, but are fine blanked, ie. stamped. Way less expensive.
They need some cleanup - the bearing surfaces of the spring and blade etc. being especially important.
The result is some variance in how low the point sits in a closed knife, regardless of blade style. I have the luxury of being able to line up five or six identical knives, to see for myself how high or low they sit. In general, they seem to vary over about 1/8". Quite a bit in the scale of knives.
I have seen the same variance in 70 year old minty Case knives, which have a good reputation for fit and finish!