On larger ships of the line with two complete gundecks (4th rate and above), the captain has his own Great Cabin, and a fancy stern gallery. The deck below has the Wardroom, brightly lit by stern windows. It is a common area for the use of the ship's commissioned officers, plus a few of the more 'gentlemanly' warrant officers such as the master, surgeon, purser, and chaplain.
Another deck below is the dark gunroom, near the waterline with no windows, for the use of mids and other lesser warrant officers.
But on smaller vessels such as the frigate Surprise, there is one less deck, and there is no bright wardroom. So the mids and warrants are bumped out of the dungeon-like gunroom and the commissioned officers mess in the Gunroom, lined with their small cabins. Because HMS Surprise is a frigate, we gather in a Gunroom.
If you happen to visit the few surviving frigates today, such as Constitution and Tricomalee, the tour guides will probably identify these officer areas as the Wardroom. This is modern naval usage, biased strongly by social senstivities. In Jack Aubrey's day, it was properly called the Gunroom aboard frigates of the Royal Navy. In the US Navy, the naming is not as clear. Aboard the large American frigates such as Constitution, the impudent Yankees often called the officer's mess the Wardroom, assuming the grandeur of a ship of the line. Both Gunroom and Wardroom were used interchangeably in the US Navy for many decades.
PO'B is consistent in his usage. In larger ships like the Leopard and Bellona, the officers mess in the Wardroom. In the Surprise, it is always the Gunroom.