You are confused because you're combining multiple discussions into one. The change you are referring to (spindle height in relation to tranny height) would mostly affect the wear and tear on the CV (constant velocity) joints that connect the transmission/driveshaft/wheel assembly together. The greater the angle they are forced to run at, the more stress they are under, so changing ride height dramatically can cause them to fail prematurely. This issue really shouldn't apply here, as we are only talking about a few degrees difference. It really needs to be considered only when making a significant change (like lift kits in pickup trucks requiring shims be put on the rear axle mounts to change the angle the rear axle sits at so the driveshaft will turn freely).
Lowering the car will affect steering geometry, but not because of this. The design of the suspension affects how much change there is in something like camber as the car is raised or lowered. The reason performance cars tend to experience increased camber when the suspension is lowered is because they are designed that way. Picture your car being thrown into a corner. The body begins to roll, and the outer edge of the car sinks. The suspension is designed so that the greater this motion, the more the tire angle changes, to keep it flat on the road even though the car is at an angle while in the corner.
This motion is very similar to what happens when you drop the car. With luck, the factory suspension can be adjusted to compensate. For an MS3, a small drop (an inch or less) appears to stay well within specs. Bigger drops require component changes to be able to get back in spec, at least on the rear end.
