Add gas to an empty cylinder. The cylinder size is still the same, so
there is no buoyancy difference in air (or indeed in water). Hence the
only difference is yes it contains more mass (atoms), and therefore
more weight as measured by a balance.

Compare with a baloon, there is a significan buoyancy difference of an
empty baloon compared to a full one, and the net effect will be
determined by the relative densities of the air (or gas) inside the
baloon compared with the atmospheric gases.

Dean