You are confusing the "els" with the elevated subway extensions that were built as part of the dual contracts of 1913-1920 or so. The els were lightweight structures that mostly could not carry heavy subway cars, whereas the dual contracts extensions were built to carry the heavy subway cars, such as the BMT standards and the IRT Low-v. Many of the original els were also connected to these extensions, but all of them are gone now. I had a whole series of photos that I took last year of all the old el connections from street level on Subchat, but alas, subchat appears to be dead. 9th Ave to Jerome Ave, 3rd Ave to WPR, 2nd Ave to West Farms, Queensborough Plaza, Broadway Junction/Atlantic/Snediker/Van Sinderen, Myrtle/Bway, and wherever else I knew of an el connection that was no longer. They are all hidden in plain sight. I did them all from my bike, starting at my home base in Brooklyn I'd take pictures whenever my training rides took me near them.
One unexpected finding was that at Queensborough Plaza there is a structure that curves away to run down Jackson St that was to be the Bklyn/Queens crosstown ELEVATED structure. It was eventually built as the IND crosstown subway. What surprised me is that I got pushback from all the "experts" but yet there it was in plain sight. The plans for the el got killed before final approval of the dual contracts, but QBP was still built with trackways to accommodate it should it ever be built. The trackways were eventually used instead to build a turnaround tail track that follows the Flushing line almost all the way to 33rd/Rawson.
Another unexpected finding, what started me on the quest to photograph everything, was that the West End line structure ends abruptly on Stillwell Avenue and the tracks curve off towards CI yards where they meet up with the Sea Beach. Everybody says that was the original plan, but I found something just the other day that tells me otherwise. At the other end, at 9th Ave, the track structure follows the tracks all the way to 9th Ave. Why would they not have built the original track structure on Stillwell the same way if it were intended to curve away?
Not everything that was built for the dual contracts is still standing either. The 3rd Ave el on Webster was an addition that was torn down with the rest of it in The Bronx. The 2nd Ave el's Bergen Cutoff was torn down when the 3rd Ave el stopped running. The Fulton el in Brooklyn was upgraded in parts but then torn down when the city took over in 1940, also some parts of the structure at Atlantic Ave were recently torn down. The Jamaica El past 121st St was torn down and put on Archer Ave instead. The 2nd Ave el over the Queensboro Bridge was dual contracts but torn down 25 years later.
All of the dual contract lines still standing were built for and operated as subway routes. The West Farms line was built as part of the original IRT subway so it is older but still maintained as part of the subway. The Brighton line is on an embankment and cut and replaced an earlier street level route.
And the F train over the Gowanus Canal? That's a bridge, not an el.