U are incorrect thinking the timing loop will change.
What i mean by this is setting the ecu into "timing mode" just locks the timing solid so it doesnt change while u are setting the base timing, by using consult etc u can read and match, eg: if the consult shows 5 degree's then set the base timing at 5 degree's. if 15 set at 15 etc.
The issue with the timing loop is alot of timing lights can't accurately read/pickup the signal. The loop wire is just an extension of the wiring going to the cylinder 1 coil signal wire.
So theoretically the loop wire should read exactly as if connected to a coil lead when run off cylinder 1 coil.
An ignition lead is 100% accurate as the timing light is designed to read it and does so easily.
You are correct that the ecu should be put into timing mode