What the article doesn’t emphasize is that the residents of other territories are similarly affected. The Commonwealth of Puerto Rico is not the only territory, there are also the Commonwealth of the Northern Marianas Islands, Guam, the American Virgin Islands, and American Samoa. Presumably the new ruling applies to residents of all of these territories.
The allegation that territorial residents do not file federal taxes was certainly true in the mid-1980s when I lived and worked on Guam for a year. I presume it is still the case, as the court recently so observed.
The U.S. was never a big colonial power, but we do have the territories indicated, and count among our former colonies the Philippine Islands, the Marshall Islands, Palau, FSM, and the Canal Zone. Several of our former territories became states, most recently Alaska and Hawaii.