The SWG will only be generating when the pump is on, so even if chlorine was the problem, it could not get back to the heater.
Check valves are needed for the trichlor tablet feeders, because they continue to dissolve when the pump is off and that very acidic water could back up into the heater.
The 3-way would allow you to select one of the other of the skimmers, but not necessarily shut off both.