A lots of things are still happening in parallel and here I'd like to present where I spent many hours by "catching a ghost". Maybe someone more experienced would spot that at once but I still do know why it's happening but fortunately I find a simple (dirty?) solution for that.
This issue is introduced with adding TPS3705-33 power supervisor and reset IC. It offers power-on (and power-failure) reset and also watchdog functionality that can be used as extreme measure if firmware for some reason blocked.