Peter Parker = Spider-Man, but "Peter Parker" != "Spider-Man".
It may or may not be true that 12345x54321 = 670592745. (I either put in the correct number there, or changed one digit in the middle at random.)
Let's suppose I didn't change it, and that you haven't yet checked. Then those two things are, really truly, equal -- they are two names for the exact same number -- but you don't know that they are equal. So the _meanings_ of "12345x54321" and "670592745" are not exactly the same, even though if "=" belongs anywhere it belongs between those things.
Philosophers call the thing that's the same the "extension" and the thing that's different the "intension" (not to be confused with "intention" which is an ordinary non-technical word). Sometimes you can safely substitute one thing for another whenever the extensions match -- e.g., when doing algebra. Sometimes you can't -- e.g., when talking about someone's beliefs.
I am not a fan of Edward Feser and I think this article is pretty wrongheaded, but there isn't anything specifically wrong with what he says about Peter Parker and Spider-Man.