NO. Smallville and Supergirl do not fit together at all. So many differences the most obvious on Smallville Kara arrived long before Clark became Superman. It never would have happened anyways. Welling never would have done it. The Smallville finale was written for him to appear in full costume for most of the episode as Superman. He rejected it, which why you got CGI Superman instead.
There's also the fact that, judging from his role on
Lucifer this season, Tom Welling has gotten much worse as an actor than he was on
Smallville. He's also gotten a bit too stocky for Superman. Let's not forget he was nearly a decade older than Clark was. He's 40 years old now.
Oh, hey, this is ironic: Tom Welling was born in 1977 and played a version of Clark Kent who was born c. 1987. Tyler Hoechlin was born in 1987 and is playing a version of Clark Kent who was born c. 1979.
It's an odd place to put a fortress. It's not as isolated as Superman's. Anyone could drive up to it.
Not many Americans realize just how vast and empty the deserts of the Western US are. Pretty much the entire western half of the continental United States consists of the densely populated West Coast, four or five big cities, and a huuuuge amount of empty:
https://eoimages.gsfc.nasa.gov/images/imagerecords/7000/7052/us_population_2005_lrg.jpg
And we saw that Sam abandoned her car and walked some distance before she reached the Fortress site. So if she's somewhere deep in northern Nevada, say, it's pretty unlikely that anyone would just stumble across the place unless they knew where to look.
Of course, I'm sure plenty of military satellites -- and Google Maps searchers -- would eventually notice this big new rock outcropping, and people would investigate. But don't forget, this is an
eeevil Fortress. So I'm sure it has more aggressive means of repelling intruders than just extreme isolation and concealment.