Master Yi and Alpha

Little confused on game mechanics here, things don't line up.

Jax counterstrike as far as I'm concerned blocks auto attacks, but it blocks alpha strike as well because it is counted as an auto attack. When using alpha with guinsoos though, it does not generate stacks. Shouldn't it, if counterstrike treats it like an auto?

It seems inconsistent. Either guinsoos should generate stacks, or counterstrike shouldn't block alpha.