Learn English – the meaning of “you has the wind of me”

Trelawney is not a peer, holder of a formal patent of nobility, or he would be addressed by the appropriate title. And he is not a JP—that is Dr. Livesey, who is three times identified as a 'magistrate'. Note that it is to Dr. Livesey that Mr. Dance first thinks of reporting, with Trelawney as the alternative, and that Trelawney generally (if sometimes with a degree of bluster) defers to Livesey.

Squire here a 'courtesy' title, accorded Trelawney by people of his neighbourhood presumably in acknowledgment of his status as the most prominent landowner of the district (that, as you surmise, is the significance of his residence being called 'the Hall', capitalized and definite-articled). Note that he has sufficient wealth to purchsae and fit out a fully-manned schooner, a very substantial capital investment. In rural England well into the 19th century such men held very great social prestige and power locally. As a class, too, they held substantial political power, since the electorate was narrow: typically only a very small number of wealthy landowners.

Trelawney's authority over Hunter, Joyce and Redruth, however, does not derive from any of these, but from his status as their employer—as does, for that matter, his authority over his captain and crew.