The reason why you don't see an issue while using Box2D is because its integration methods are low-error. A simple platform game using Euler style integration of the type

   each step, add forces from input and gravity. add the resulting acceleration multiplied by time to my position.

will trivially produce jump heights of 50% variation when subjected to a variable timestep. On a quick search, Box2D uses semi-implicit Euler [0], which much more accurately fits the curve. It does not guarantee zero error: to do that you have to have an analytic method, which isn't applicable to a general-purpose physics simulation.

[0] https://en.wikipedia.org/wiki/Semi-implicit_Euler_method

edit: i did forward euler wrong