It’s really a showcase of how very high IQ and outstanding mathematical abilities mix with a distrust of existing technologies and a lack of expert intuition coming from more normal industry experience.
Just try implementing MTProto, or at least read the low-level docs, and you’ll see for yourself. Crypto isn’t the weirdest part. The whole thing is an attempt to define a binary protocol in terms of grandiose mathematical concepts most of which didn’t even end up ever used in the actual protocol. And there’s zero thought given to what’s actually important, making a bullet-proof syncing between server and client states (and that results in numerous bugs to this day).
Can’t discount malice, but I don’t believe that’s the case.