I respect your position as a canon purist, and you are free to disregard "Darkness" completely.
I like to think of it as Randall's head canon, and with "Darkness" as context, many of the other hints about the Ebon Magistrate's unexpected prowess and the MoC's mysterious tech source fall into place rather neatly. Without "Darkness," they're still black box mysteries.
I wouldn't say I'm a canon purist but again..."head canon"
You cannot be sure he wrote that story the way he did because it was non canon and so he was free to indulge, crafting a story that would never be canon and therefore free to explore.
In the same way, you cannot take the out of game hints that the Wolverines ate the MT as canon because until it is written down as anything other than in game rumour,it is subject to change.
And yes...they are mysteries and until Darkness is canonised, it really can't be considered in a discussion of canon events, or even possible events.
"IF Darkness were canon" is suited for discussion, but it shouldn't really be used to support or counter arguments arising from the canon BTU.
So what if the Ebon Magistrate is proficient? That doesn't need the Minnesota Tribe...it requires hard work.
Strange new tech? A hidden research base even ComStsr didn't know about or the discovery of SL era base or ship
There is nothing in the mysteries or rumours that require the MT to be around in order to be explained. No reason to go hunting for conspiracy theories.
Darkness may someday be canonised.
Today...it isn't and even creative interpretation of the story and background can't really save it. Either the events happened as they are depicted, or they didn't and the MT link only holds if they did.
And even if it is canonised, it doesn't need to be the Wolverines.
It could, as one example, be IntelSer, swapping meaningless technical information in exchange for a treasure trove of data. That fits in better with the use of the "Well bargained" phrase