[llvm] [llvm][yaml2obj] Modify section header overriding timing (PR #130942)

[Fangrui Song via llvm-commits]

MaskRay wrote:

I forgot what ShOffset did and I was confused when reading the commit message for the first time...

Consider incorporating the following to the description.

> `setProgramHeaderLayout` uses section offsets for determining p_offset. Move section header overriding after `setProgramHeaderLayout` to prevent `ShOffset` from affecting program header `p_offset`.

https://github.com/llvm/llvm-project/pull/130942