However even in the the TNG/Voy/DS9 era transporters are generally only used to beam between ships or down to planets.
The issue is that we didn't see Scotty invent this during TNG/VOY/DS9. Future-Spock came back from later in the 24th Century than any of the previous shows/movies depicted. Future-Spock hails from 2387, whereas Voyager ended in 2378, and Nemesis occurred in 2379.
Scotty was rescued on a Dyson Sphere by the Enterprise-D in 2369, and sometime in the decades between that and 2387, he invented transwarp beaming. We just never saw this. It either occurred off-camera while one of the other Star Trek series/films was happening, or it occurred in the ~decade afterwards before Spock was sent back in time to the alternate timeline.
How could Harrison use technology Scotty would develop to beam 90 light years when the same technology isn't available after Scotty's death in the prime universe?
Scotty's not dead. He invented it off-screen, or after Nemesis, which is the latest film in the prime timeline (excepting the flashbacks in Star Trek (2009)). Future Spock brought this technology back in time, and gave it to young Scotty, who in turn gave it to Starfleet. Starfleet/Section 31 then built a transwarp transporter, which Harrison stole and used.