Supposedly, the Yorktown
was not operational when the Probe departed. The silencing of the Saratoga
involved fireworks going off on the bridge; if she and the Yorktown
ever were salvaged, then installation of all-new bridge consoles and other fried components would be quite likely. And something of an integration nightmare, no doubt.
Sure, the E-A is different from the E-nil-refit. But not necessarily "newer" in the specifics. Rather, she could be a hodgepodge of older, "less refitted" tech inherited from the Yorktown
years (the old-fashioned shuttlebay and the GNDN tubing), and modern duotronics replacing the stuff fried by the Probe. Plus some new vanity covers in the corridors, the old ones having had to go to remove the stench of the corpses.