Using a kinematic model is fine as a first step to understanding some of the geometry of vehicle suspensions. A simple link calculator which is geometric or kinematics based like the ones you see referenced all the time in the 4x4 forums is not very revealing when it comes time to actually building a suspension. Taking the springs out and moving the axle around is kinematics. The way a vehicle’s suspension works is based on a “Force” model and not a kinematic model. A force based model does not necessarily follow the principle of instantaneous centers because the magnitude and direction of forces are ever-changing. The static numbers calculated bears little resemblance to the dynamics of a vehicle’s suspension. Geometry is only a part. Stiffness distribution between the front and rear, wheel rate, corner weight, shocks, and anti-sway bars all affect the forces seen by the geometry. None of which are accounted for in a geometric calculator.
Changing the axle control arm mount locations relative to the centerline of the axle does indeed have an effect on the forces seen by the control arms. Moving the lower control arm up on the axle increases the force it sees because of the gain in leverage relative to the tire's contact patch. Simply stated, the joints and mounts on both ends must be strengthened. If some of the separation of the links at the axle is lost, the forces seen by both the upper and lower arms will increase. That means bigger joints and mounts on both ends.
If the separation at the axle is maintained or increased, then the same or smaller upper joints and mounts can be used, but the way the mount interfaces with the axle will have to be stronger. This is the common failure point when extending the upper mounts to just maintain the existing sseparation. Locating the upper arm on the diff side helps in creating a stronger interface.
If raising the axle end of the lower control arm increases the amount of force it sees, and the force is transferred to the frame/body, then the suspension dynamics change. The same thing happens with an off-center three-link. More force is carried by a single arm, instead of two, and deposited asymmetrically. That affects the suspension dynamics and requires stronger joints and mounts, too.
Changing the angle of the arms in relation to each other or changing the pivot points or the length of the arms will all have an effect on pinion control in terms of degrees and the rate of change.
These are just some things to think about and not pointing out anything specifically wrong. Everything you do to your suspension has an effect and it’s usually a compromise with some other characteristics. If you can’t find the compromises then you’re not ready to make the changes. The rock-grabbing lower control arm mounts were not an oversight by some lazy engineers.