I have worked on these quite a while and I do think that the reasoning behind this design is so that the codes could not simply be cleared before one went for an emmission testing in some states . Notice that these with the DM [N59 module] are Cal vs Fed systems.
If there has been a CE lamp trip, they want it to be verified as Fixed rather than just cleared , I suppose.
It took me quite a while working with these and monitoring when the single would finally show up before coming up with this conclusion, but then I did find a couple of mentions of it from different data and it seems to confirm it..
{ All-Data has a piece on it ]
The other modules do not need this protection as they are simple fault diagnosis for other modules , whereas the CE is indicator to both owner and Inspector that Emmissions faults have been detected.
These OBD1 systems were in the transitional period to OBD2 and that is why they are capable of both Flash and digital readouts .
I have also tried a MT2500 scanner on pin 3 [same as built-in led. DM] and found same results.. you simply have to wait for reguired drive cycles/self test of ECU of Emmissions system ..
One good thing about the scanner over the flash is the modules on these do have the capacity to monitor misfires and injectors individually, etc .