The rate difference is because they get 800NTD/day subsidy from the government for a quarantine guest if the person is a citizen or permanent resident. If you are not a permanent resident or citizen, you cannot get the cheaper rate.
When I went to the Taipei quarantine hotel list, most of the hotels show the same rate now for citizens, APRC holders and foreigners. Not sure why that is, unless maybe the subsidy ran out.
Does anyone know if there are Taoyuan quarantine hotels? It’ll be nice to have more room to stretch out for those 15 days and not pay the big city premium price lol.