Dynamic linking makes it possible for executables to share a single copy of system frameworks; this saves physical memory, improves performance (due to reduced cache traffic), reduces the size of downloads, etc.
The UUID allows the debugger to reliably associate an executable with the dSYM bundle containing debug information.
Other features not discussed in the article allow a single program to run on multiple architectures (PPC, I386, X86_64, etc), allow the system to reliably determine whether a program has changed, to decide what capabilities the program has been granted, etc.
It's worth putting these size number into perspective; yes, EIGHT THOUSAND BYTES sounds big and scary next to twenty, but the overhead scales linearly with the number of executables and their functional complexity, not geometrically. Also, you have on the order of ONE TRILLION BYTES of storage for these headers, rather than three hundred and sixty thousand...