While not a in-universe reason as to why its not the MwBoS, I find it unlikely to be the MwBoS simply because they aren't made by Bethesda. Like it not, real world politics comes into play in where stuff shows up.
Bethesda gave Obsidian all of the Western United States for use in New Vegas, since people at Obsidian made Fallout 1&2, which were OFC set on the west coast, and Obsidian did use it all.
-The NCR is still in California, Nevada, and Oregon.
-The Legion is in Arizona, New Mexico, Colorado, and Utah.
-The northwest states like Idaho, Montana, and Wyoming, are said to be mostly wilderness and in ruins.
However, Obsidian never strayed beyond that territory, even when it doesn't really make sense. The Legion for example has been conquering stuff for the last 30 years, and has held all of Arizona and New Mexico for some time. Yet despite this, and despite the fact the New Mexico/Texas border is hundreds of miles long, and despite the fact several major Texas cities, such as El Paso, are just miles from the border, and Amarillo, and Lubbock, are just 70 miles from the border, no one in The Legion mentions going into Texas, or conquering any towns in Texas, despite the fact that doesn't really make sense given how expansionist The Legion are.
We hear about Montana, Wyoming, Colorado, and New Mexico, but we don't hear about the Dakotas, Nebraska, Kansas, Oklahoma, or Texas. Basically, its as if a giant invisible wall came up and drove everyone away from that direction. And you know what? That invisible wall matches exactly with the border between the western U.S. and the Midwest/South.
Similarly, Bethesda have said they are east coat people, and in Fallout 3 and its DLC we hear about places all up and down the east coast. However, when we go to the Pitt, the remnants of Pittsburgh in the very western part of Pennsylvania, all we hear about are places like Erie, Ronto, D.C., and the Commonwealth, all of these places are north, north east, or south east, of The Pitt. We never hear about any places to the west of The Pitt, despite the fact Ohio has many major cities in it, all located far closer to the Pitt then Ronto and The Commonwealth are, and all of which would make for more relatable references then the small town of Erie.
And you know what? The Pennsylvania/Ohio border is the exact border between the east coast, and the Midwest. Much like Obsidian did in the west, Bethesda did in the east, and basically drew a big line in the sand, and generally left everything on the other side of the line alone, outside of token references to the locations of other games.
I highly doubt its the MWBoS in Fallout 4, becuase the Midwest, and the things in it, aren't part of Bethesda's turf, and they have so far seemingly tried to saty out of other people's turf. Obsidian has their west coast, Bethesda has their east coast, and the midwest is that land of "other people's stuff we both admit is there, but we don't really want to mess with since it isn't ours".