V-brakes, ----This changes everything.

While V-brakes have spring adjustment screws to center when open, the forces when closed depend of simple geometry.

A quick physics lesson---
Each arm is a simple lever. Newton's third law dictates that the force applied at the end of the lever is equal. So the force at the brake shoe is determined by it's distance from the fulcrum (aka pivot bolt). If either shoe is lower than it's mate it will push slightly harder moving the rim over until the wheel's stiffness resists.

Minor flexing is normal and acceptable, because bicycles don't depend on being perfect to work. But if it bothers you get raise or lower one shoe to balance the braking force.