I am all for believing that the system still fully functions. If you did not know how to test it, no one can tell if the ECM is in bypass or not.
The bypass mode has been used for ages at HD and that led to some bikes growing feet. When I worked with them is when I found that a quick and simple jumper wire would get around the system if it had been bypassed in the ECM, so it is a concern when ECM's are being exchanged. This is just why the linking process takes 10 minutes at a dealer and 30 minutes if you do not have DT to do it with. It doesn't need to take that long at all but the long delay is written in the software to keep bikes from being taken quickly by simply plugging in a different ECM. If you do not have the HD security system then this does not matter.
If you would like to check all you need is a short jumper wire. Unlock the Ign. but take the key fob about 10' away from the bike. Turn the Ign. on and the run switch on then jump the starter from the battery post on the starter to the solenoid terminal, these are about 5" apart on the starter. If the bike fires up and continues to run the ECM is in bypass, if it starts and stalls it is not. Take this as nothing more than a CYA as that is all it is meant to be.