Remember that part of the remit of Ideal Flight is to test the system very thoroughly in all aspects of the simulation. It's used to check that a system is good to go. Generally those issues that arise on particular systems or aircraft are showing that there's likely an issue with that system or addon.
As example: Ideal Flight always starts the flight from a saved file but without Ideal Flight we go into the scenario builder and select a plane and go into the simulation. Those are very different situations, the start from file is way more thorough and can fail with undercooked addons.
Remember also that simulators don't all work the same. With P3D v4 that can't restart the autopilot from a saved file if the sim is not running and the saved file is passed in to the command line to start the simulator. With P3D v5 this issue has been fixed. I got a lot of mail from that situation but it was a fault in Prepar3D. For some that's hard to believe. In Ideal Flight there's some other test procedures called Startup Behaviour, on the startup page popup menu, those can start the sim from cold and have the autopilot running as well. But those behaviours are more for development and testing addon aircraft. Again I had mail pertaining to those behaviours apparently "not working", but it was a situation arising from an undercooked addon. Ideal Flight was simply doing its job of go/no-go gauge.