Why does the price change when I modify the logo dimensions?

Short answer: The cost of a marking depends on the rectangular surface of the logo, and it goes by tiers. Crossing a tier changes the price of every product that uses this version.

A price set by surface tiers

The price of a marking is not proportional to its size: it is set by rectangular surface tiers. As long as you stay within a tier, the price does not move; the moment you cross out of it, it jumps to the next tier.

The rectangle is what counts, not the drawing

The surface that counts is that of the rectangle around the logo, not that of the drawing: the marking is printed on a film cut into a rectangle, then heat-transferred — that film and the ink are what get used up. See What is a logo version and why are there several.

The change applies to every product in the shop that uses this logo version, not only to the one you are configuring right now.

Going further

What is a logo version and why are there several — why the tiers exist.
How do I change the size of a logo version — when to modify a version, and when to create a new one.