GLFW isn’t really designed to be used in a program which already has other windows opened, and so it sets the process DPI awareness which is likely what causes the other windows to change. See the code in _glfwInitWin32:
You can use the GLFW_SCALE_TO_MONITOR window hint to ensure GLFW scales it’s windows to the monitor for you automatically, but this will not apply to the already created windows.
Without altering GLFW one solution would be to initialize GLFW before creating the other windows and then setting their size/scale (if possible) using the monitor content scale.