Has anyone seen 荘 kanji written with the primitive earth instead of samurai. I found this SOD but I presume it's wrong, since everywhere else is written with samurai primitive.

Guess the only compound I know is 別荘... rare?

別荘 is not a particularly rare word, but the kanji isn't used a whole lot outside of that word.

As for the stroke order diagram above, I think it's just a mistake although there's always the possibility that it's a variant character or a Chinese variant.

That's an optical illusion, they're actually the same length!