Totally out of left field, but a couple thoughts on this (which have all been mentioned by others in other places):
1) The 9ers seem to be emulating the Broncos model in which they have a former player who is the face of the operation, but the actual nuts and bolts GM work will fall on other people (Marathe does cap and contracts, Gamble does player eval, there's a rumor they're bringing in a 3rd guy to split up pro player personnel and draft personnel). If that's what they're doing, it explains why they were also looking at media-side guys in the GM search, as they want someone with some media savvy to start representing the org.
2) 9ers fans have been begging for someone between York and the team. This could very well be that..
3)...or not. I don't think we can really make a statement about what's going on until we see the organizational hierarchy chart (if Paraag is parallel in the hierarchy with Lynch in reporting to York watch out, this is just going to be more of the same).
4) Shanny really had the 9ers by the short and curlies, which I think really limited how attractive this job was. They might be using this org structure because it's the only org structure that would still allow Shanny to have final say on the 53.
5) I think the six year contract is easily explained: It means Shanny was able to get a six year contract, and they don't want to put the GM on a shorter contract than the coach, because that's just going to lead to the same power problems they've already had.
6) And on six year contracts, once again, and as if we need any more proof, Jed York is an idiot, not cheap.