Sell/Cover vs ApplyStop vs Backtester settings


I'm into AFL from past few months, i have a question on exiting positions. As per my understanding we can exit a trade in one of the 3 ways

1) Sell/Cover - We can exit Long/Short positions by coding logic for Sell/Cover. We can use this to exit open positions either at Target or Stop Loss levels
2) ApplyStop - We can use this feature in AFL to define rule based exits by coding this into the AFL.
3) Backtester settings - We can select options under 'Stops' tab in Backtester settings.

Now my problem is - If we use option 2 or 3 (ApplyStop or Backtester settings) the Sell/Cover is not triggered, hence i am finding it difficult to eliminate repeated Buy/Cover signals which i could have done using ExRem(Buy,Sell); or ExRem(Short,Cover); if the Sell/Cover was happening at the point where ApplyStop/Backtester settings trigger stops.

Is there any way i can overcome this by limitation of using ApplyStop or Backtester settings?

Also can someone please tell if using ApplyStop or Backtester settings to define stops work in real time automated trading also or is it limited only to Backtesting?

Thanks a lot

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