You are right that the volume of individual molecules will vary, but when we talk about the volume of a gas, we are most interested with the space between the molecules and not the molecules themselves. When we deal with gases in chemistry, it is often useful to think of each gas molecule as a tiny point in space with an imaginary sphere surrounding it. Each sphere can hold only one particle, and no two spheres can overlap.
In physical terms, these spheres represent repulsion forces between the different gas particles in a given sample. The spheres themselves are much larger than the gas molecules, and interestingly, the sphere size doesn't change much as the size of the gas molecule changes (assuming ideal behavior). In other words, the volume of the repulsion sphere for a
To clarify, suppose we have a situation as in the image below of red gas molecules contained in a box of volume