The resolution is still 16 bits in either case, because the resolution is determined by how many bits the ADC is designed to produce; but there can be an advantage to using an appropriate gain stage.
The 90V/V gain stage reduces the effective LSB step size (from \$ \frac{5~\text{V}}{2^{16}}=76~\mu\text{V} \$ to \$ \frac{5~\text{V}/90}{2^{16}}=0.84~\mu\text{V} \$ as you suggest), and also reduces the dynamic range by the gain factor (from \$ \pm2.5~\text{V} \$ to \$ \pm0.02778~\text{V} \$ ).
Reducing the dynamic range at the input is good, when it is a better match to the actual dynamic range of the input, so that more of the ADC's fixed digital range is mapped to useful signal.