Because that house, the origin, that backstory, and family was perfectly fitting to Connery's Bond.
First, Bond is Scottish and his family is canon. So yeah, it fits all Bonds.
The house in no way invokes anything we have seen in Bond. Nothing. There has never been an house of usher in Bond.
The backstory and family fit Craig's Bond to a tee. Go back and watch Casino Royale. Watch the scene on the train specifically.
Craig's Bond has always been the maladjusted orphan. No Bond before him even touched on it, let alone to the degree they have with Craig's Bond. Craig's Bond bleeds it. There is a part of him that can clearly mingle with the upper class. He was clearly "raised right", but he always has that sometimes angry, sometimes cheeky, and sometimes rueful smirk.
When he is standing there looking out of the land in front of the Aston or through his window, that is Craig's Bond. His relationship with M as his surrogate mother, that is Craig's Bond. As he walks into that house and all the different emotions hit him, that is Craig's Bond.
Did we ever see Connery do exactly what Craig did? No, because the people who wrote Skyfall aren't idiots; they're not going to just copy the ending to another Bond movie in. They wrote something original, they wrote something very good, but that third act is tailor made for Connery's Bond.
In what way? When was Connery's Bond ever an action star in the way Craig's has been? When was Connery's Bond ever a tough, almost thug that could put on airs convincingly?
Moreover (not that I expect people to really understand this bit, as art direction is rarely focused on or talked about), but even the art design and direction changed dramatically in that final act. In fact, I'd contend the color palettes, set designs, and lighting were much more akin to Connery's movies (hell, just look at the new cover to Goldfinger, it looks just like that final act's scenery) than it does the first two thirds of Skyfall.
I am an art direction kind of guy, but there is nothing about the color palette or set design or lighting that invokes Connery's movies. Where are all these scenes that look similar? Connery's Bond was all exotic locals, clear skies and color.
Skyfall's finale is foreboding and intimidating, with a lack of color. The fog adds to is isolation. In invokes what Skyfall means to Bond.