Yes, the size change for a molecule is virtually non-existent relative to the space it (the molecule) has to bounce around in in air. Short of tossing a molecule into the sun, where it might fragment, you won't see enough change to make a difference to anything that would concern a pilot.
However, the density of air has a lot to do with lift generated over an airplane wing, and altitude affects that. (Higher altitude = less air = lower density)
Also, temperature does affect the density altitude. When it is hot, there are fewer molecules in a given volume of space, so the density is lower, and you get less lift.
Humidity affects density altitude too, as water molecules weigh less than nitrogen or oxygen molecules, so provide less lift. (Never checked on the physics of that however.)