Speculation: Would John F. Kelly have been the one to suggest funneling stuff into that server?
His previous positions meant that he would have been aware of those systems and he was CoS after Preibus was ousted in July 2017 and was in there until this year and had previously been DHS head.
https://www.theatlantic.com/politics/archive/2018/12/john-kelly-white-house-chief-of-staff-leaving/569779/
https://www.buzzfeednews.com/article/jasonleopold/john-kelly-dhs-official-email-foia-public-scrutiny
= new reply since forum marked as read
I think people might recall his bragging about "all the generals" that had been brought in. I think all of them are gone now. 
He was known for side-eyes and face-palms during his tenure. 
might be in the Mueller report but was redacted out. There were pages and pages that were blacked out - especially the stuff about Stone (and probably some about Manafort) because Stone's prosecution is ongoing with a trial supposedly due to start in November.
Some Stone connections to the latest revelations - https://www.emptywheel.net/2019/09/25/how-roger-stones-trial-relates-to-the-ukraine-scandal/
by hiding the evidence would have needed to have been done behind his back...
from back in the old days (decades ago) when he was a U.S. Attorney, but he would have had little or no knowledge about, let alone access to, the newest and more top secret stuff and where that was housed. Kelly had been DHS head and Commander of the Southern Command prior... Also he apparently had issues with how DHS was configured and was being run - https://www.businessinsider.com/john-kelly-homeland-security-a-mess-trump-dhs-2019-4
But one thing that I just saw in the link in this post, was mention of the name "Stephen Miller" - now THAT one is the devil and I wouldn't be surprised if he directed the operations and helped to engineer the coverups.
he had a tendency to be a braggart and a blabbermouth and some of them seemed to want to be a "firewall" to that behavior. But there came a point where they couldn't even take it anymore and/or were summarily "fired" and that was the end of that. 
As I noted - it's speculation mainly because there were few in there who would have been familiar with these top secret systems... However, knowing that deleting these damning records would have made things worse, then a decision was made to "retain them" but do so in a covert way, perhaps with the intent to come up with a "justification" later as to why they were put into such a place.
Every one of these data systems have some kind of audit trail/log for who was accessing them and when, so there will be plenty of records to be poured through.
Again my speculation would be about who in there would have had knowledge of such a system and it could be that the info about the existence of these various security systems may have come from him but perhaps someone else - like Miller - may have been involved in giving orders.
AND another one who has gone far far underground and who hasn't been mentioned, is Sessions. Sessions would have probably been aware of some of these systems too and as much as he was supposedly "recused", the question might be how much was he really "recused" and was he doing other stuff behind the scenes until he was dismissed? 
Wondering what, if any, of this code secret stashing McGahn knew and/or ignored.
The mind reels with best laid webs of spiders and minions.
(and he keeps getting "blocked" with the bogus "executive privilege" argument)
But I was just looking for one thing and found some wild stuff from 2017 about those earlier WH lawyers - https://www.npr.org/2017/09/19/552169759/obamas-white-house-counsel-weighs-in-on-trumps-lawyers
Marc Kasowitz
John Dowd
Ty Cobb
It was a zoo in there!