Well, the total cost was reported as $190 million, so after the 1000 people get 100k, there is still 90mil to account for...
I'm probably not up with the times, but I don't really see many actors in that film that would be classed as A-list (although the definition of that is somewhat loose).
I really like Keanu, and he seems like a great guy, but I don't think he getting paid $20 million a film, although his popularity seems on the rise again (but perhaps that is just on Reddit). He was reportedly paid 2.5mil for some of the John Wick films, and you'd have to imagine he is the top paid in this latest matrix film.
Regardless, I have already said I don't know much about the industry, and I haven't even seen the film, so it is all just speculation on my end. However, I'm willing to bet that a significant percentage of the reported spend went to subsidiaries charging healthy margins, which is common in the industry to help cut into the % of profits the studio would have to share with people as part of their contracts.