Is this simple reflective separative theory inconsistent?

Yes, this theory is inconsistent.

We note that by 1 and 2 that if set(x) and y⊆x, then set(y).

(a) There is a v such that ∀x(set(x)-->x∈v).

Proof:Suppose not. Then ∀v∃s∃t(s∈t∧s∉v). By 3 there is transitive x such that

  set(x) and ∀v(v⊆x-->∃s∃t(s⊆x∧t⊆x∧s∈t∧s∉v). In particular 

  (x⊆x-->∃s∃t(s⊆x∧t⊆x∧s∈t∧s∉x).  But this is impossible.

Suppose that ∀x(set(x)-->x∈V). Then ∃w∀t(t∈V-->t∈w). By 3 there is transitive x

such that set(x) and ∃w(w⊆x∧∀t(t⊆x∧t∈V-->t∈w)). Since t⊆x implies set(t),

t⊆x implies t∈x. By 2, there is a c such that t∈c<-->(t∈x∧t∉t). Since set(c),

c∈c<-->c∉c.