So by then the system is full without the need for the compressor to draw the gas round.
No it is not. Gas is fed into the low pressure side, initially pulled in by the vacuum. When there is sufficient pressure the compressor starts up and fills the high pressure side fed by pressure from the gas bottle. There are segments on the gauges that indicate low normal and high pressure. You continue to fill until the gauge shows high on green normal zone but just short of red overfill zone. You then close low pressure valve to stop fill and disconnect gauges. Done it many times. Of course you do have to have the filling gauges and pipes along with a vacuum pump.