EM - You might want to crawl under your car to visualise things and recheck your statement.

The shock plates (and springs) get lowered the same amount the body is (Lowering blocks go in-between rear axle and leafsprings+shock-plates).

In short, it's only the rear axle that ends up higher 'in' the body/suspension, everything else stays the same.


edit:
Tree'd by the Guitar man