In Spider-Man: Into the Spider-Verse (2018) Alternate Universe Cut, Will Gluck is doing the commentary for "Spider-Man: The Motion Picture":
Will: And we have a very special guest on the commentary, a consultant for the film. His voice has actually been altered to protect his identity, the actual Spider-Man.
Why is the identity of the actor voicing Spider-Man kept secret even in the commentary?
The voice has been altered because, as Will says, the person doing the commentary isn't the actor of Spider Man from the movie, but the actual Spider Man, who was a consultant on the movie, and his real identity is a secret.
Spider-Man: The Motion Picture is an in-universe movie that Miles and Ganke watch (with director commentary turned on) in the Alternate Universe Cut of Spider-Man: Into the Spider-Verse. In Miles' universe, Spider Man is a successful superhero with a lot of merchandise (including the movie they're watching), but his civilian identity is still a secret. So although the real Spider Man was a consultant on Spider-Man: The Motion Picture and also speaks on the director's commentary for that movie (along with director Will Gluck), his voice was altered in the (in-universe) commentary to preserve his secret identity.
If I'm following this correctly, this is commentary on an in-universe movie, inside a deleted scene from the actual movie.
The quote you've included doesn't say that this is the actor playing Spider-Man, but a "consultant for the film". The implication is that in the universe you're watching, Spider-Man is a real person, who consulted on a movie about himself without giving up his real identity. The commentary is all happening inside that universe, with the voices of Will Gluck and the real Spider-Man.
In the reality where you're watching the DVD, Will Gluck is a real film director, so is acting as his own alternative reality self; but there is no real Spider-Man [citation needed], so the part is played by an actor.
