I understand you're point of view Dave but what you are saying is both at odds with professionalism, and also the way things are done by AFL, RL and Cricket. In all these sports, once professional contracted, the players alignment changes to a club in the tier below which is either aligned to the professional club, or in it's region.
You have to look at it from the Super Rugby franchises' point of view. They pay these players and their success is tied pretty heavily to them. If they are back in Sydney and playing they cannot monitor their physical state. When these players are injured they are not able to assess these immediately. The Brumbies move to make all players play in Canberra was due to this. 3rd tier only extends the need. Imagine if a player has a knee injury for example, the 3rd tier club with likely inferior facilities, differing interests, located in a different state, doesn't manage it to the requirement of the Super Rugby franchise and that player post 3T season then has an op and recovery that causes them to miss Super Rugby.
Injuries cannot be avoided however the franchises have the right to manage injuries to their paid resources the best they are able to.
This is a 3rd tier comp, not state of origin. The next best tier of players, wherever they are from need to play. What would be the benefit of inferior Perth/Melbourne players getting a game and superior Sydney/Brisbane players not getting a game?
AFL players when not playing AFL play for their clubs aligned state league team, NRL players do the same. Cricketers not playing state play club cricket in their state since they live there. How is rugby any different?
These other sports all have local clubs that develop players. It all survives because clubs that the best players come from attract more talent based on their club's record in developing talent, as do professional clubs.