Why would splitting a password output be better than separate HMACs for encryption/authentication key derivation?
Internally scrypt has a huge state space, from which it derives 256-bit output blocks using PBKDF2-HMAC-SHA2, so it's basically already doing what you suggest as 1., just with much larger inputs. Adding another level of HMAC on top will not help.

In general, you need to be careful when chaining hash functions like $H_1(H_2(x))$. Both collisions in $H_1$ and those in $H_2$ lead to collisions in the combined hash. With a 256-bit hash you are still safe, however, since even doubling collisions gives you plenty of security margin.

If both are secure, but just using scrypt is simpler, why not use what's simple? That makes it less likely there's a mistake.