Technically the mattes are high enough resolution too.
That's not true. The bluescreen compositing they used required using second- or third- or later-generation images that were degraded in quality from the original film elements. (When you rephotograph a photograph, the graininess increases, and optical compositing often required rephotographing the same film elements multiple times.) Also the matte lines become more evident in high-definition.
If they still had the original, individual film elements that were shot for TOS, they could've recomposited them in high definition, since the original film elements would be in full, undegraded resolution. But my understanding is that those weren't preserved, which is why they had to replace the whole shots with CGI.
I don't know if they did tabletop miniatures in TOS-R...
If you mean in the original TOS, no, I don't think there were any tabletop miniatures. Cityscapes were all either Albert Whitlock matte paintings or dioramas/backdrops in the background of live sets.