The difference is in the way the OS sees the buttons. The buttons that are directly bound by AEBPlus to a hardware button bypass the OS, e.g. although device lock (a part of the OS) is supposed to grab the buttons and block them when the device lock app is running, AEBPlus is quicker and enables the buttons. So, when device lock is running, the buttons that are grabbed by AEBPLus bypass the OS and Device Lock and the applications still pop-up despite the buttons being locked. This behaviour is annoying me, since when I use device lock I expect my buttons to be safely locked when my device is in my pocket. This is not the case when you bind them directly with AEBPlus, instead although the buttons are locked, several apps were opened when I took the device out of my pocket and a call had been made.
However, when I create a "virtual button" with AEBPlus, this button is seen by the OS as a normal hardware button and is disabled by Device Lock. So, when I lock the buttons with device lock and put the device in my pocket, an accidental press of the button causes AEBPlus to activate that virtual button, which is then blocked by Device Lock. In this way, my buttons stay safely locked when the device is in my pocket and prevents apps opening due to accidental presses.
You can still use the multiple key presses of AEBPLus. Instead of directly assigning an application to a double press with AEBPlus, I assigned a virtual button to a double press. Then in start-settings-buttons I assigned an app to that virtual button. I have done the same for tripple presses and press-and-hold.