At the beginning of The Matrix, the WB and Village Roadshow logo sequences are given a green, flickery appearance that is clearly styled to fit the movie.
At the beginning of Serenity, the globe from the Universal logo becomes Earth-That-Was.
What are the first chronological examples of both of these devices?
I don’t know if it was the actual first, but the first I can remember seeing is in Raiders of the Lost Ark, when the Paramount mountain logo turns into a real mountain as the movie opens with Indy in the jungle…
The Marx Brothers movies played with the MGM “Leo the Lion” opening. A Night at the Opera had the three Marx Brothers (Zeppo was out of it by then, although virtually replaced by Alan Jones) “roaring” through the “Ars Gratia Artis” frame. the silent Harpo was supposed to reach into the film/foliage and retrieve his trademark horn to use.
They played with the logo in another film – normally the Lion is matte into the frame, but for this opening they actually had the lion behind a cutout, and after the roar the camera dollies around behind it, where you see Harpo with it.
MGM also “played” with the logo by having Tom of Tom and Jerry hissing through the opening instead of Leo
The Pink Panther, too:
Anticipating the "Matrix" opening the OP lists, in 1959 they surrounded the Leo the Lion with the same odd green used in the opening credits of **North by Northwest**:
For **The Fearless Vampire Killers** Leo morphs into a fanged vampire:
So MGM has been screwing around with its trademark logo, changing it sometimes to fit the movie, since the mid-1930s, long predating paramount’s Raiders of the Lost Ark.
By the way, Paramount replaced the m,ountain with Mt. Sinai in its opening for 1956’s The Ten Commandments
No help for you in terms of going back earlier, but I do remember a couple of fun ones were done for Waterworld, where the Universal logo was covered in water, and then one that the Internet suggests was The Cannonball Run, when the Fox logo had a car chase all over it.
Here’s the “Mt. Sinai” opening from 1956’s *The Ten Commandments:
https://www.google.com/search?q=Paramount+logo+%22The+Ten+Commandments%22&biw=1920&bih=934&tbm=isch&imgil=luIHg8VVnD3JCM%253A%253BDXG8oJc5_fvaEM%253Bhttps%25253A%25252F%25252Fwww.youtube.com%25252Fwatch%25253Fv%2525253DgmV2TCtQwxo&source=iu&pf=m&fir=luIHg8VVnD3JCM%253A%252CDXG8oJc5_fvaEM%252C_&dpr=1&usg=__-NhLOM6C10QBwcTukEbYDCLkims%3D&ved=0ahUKEwjW9InMmZDKAhVL5yYKHV5LBTUQyjcILw&ei=JmuKVtbJN8vOmwHelpWoAw#imgrc=luIHg8VVnD3JCM%3A&usg=__-NhLOM6C10QBwcTukEbYDCLkims%3D
I have a suspicion that Steven Spielberg might be responsible for using the "Paramount logo changes intoi the mountain" in *Raiders of the Lost Ark* precisely *because* of this opening. Spielberg clearly had a "thing" for The Ten Commandments -- it's playing o the TV in the background as Roy Neary Richard Dreyfus) is building the model of Devil's Tower in his living room*, echoing his efforts. In addition, the Ten Commandments' special effects are echoed by those in Raiders, especially the Angel of Death. So it wouldn't surprise me if he was inspired by the specialized opening logo, too.
*“Gonna build a mountain
In my Living Room”
as the mailboxes sing in the parody Closet Cases of the Nerd Kind (at 5:42)