Provided always that the said American vessels do carry and land their Cargoes in the United States only, it being expressly agreed and declared that during the Continuance of this article, the United States will prohibit and restrain the carrying any Melasses, Sugar, Coffee, Cocoa or Cotton in American vessels, either from His Majesty's Islands or from the United States, to any part of the World, except the United States, reasonable Sea Stores excepted. Provided also, that it shall and may be lawful during the same period for British vessels to import from the said Islands into the United States, and to export from the United States to the said Islands, all Articles whatever being of the Growth, Produce or Manufacture of the said Islands, or of the United States respectively, which now may, by the Laws of the said States, be so imported and exported.
The treaty also prevented American vessels from carrying West Indies trade anywhere but to the United States and back.
But it is expressly agreed, that the Vessels of the United States shall not carry any of the articles exported by them from the said British Territories to any Port or Place, except to some Port or Place in America, where the same shall be unladen, and such Regulations shall be adopted by both Parties, as shall from time to time be found necessary to enforce the due and faithful
In other words, it basically gave the British free reign to aggressively pursue and maintain the very same colonial trading pattern that Hamilton disingenuously cited as a justification for his protective policies in the Report on Manufactures.
On top of that it also obliged the United States to pay certain British claims on merchant vessels seized as prizes of war by France and sold in the U.S., thereby giving favoritism to Britain over France in their ongoing war rather than maintaining a position of true neutrality.
Nothing quoted shows this to be an alliance. Nor did it change much.