In 「彼はまだ来ない」, the focus is on the action of coming.
The meaning of the sentence is close to:
He hasn’t come yet.
He hasn’t arrived yet.
In 「彼はまだ来てない」, the focus is on the state of his being here.
The meaning of the sentence is close to:
He hasn’t been here yet.
He isn’t here yet.
When I was asked 「鈴木さんは、“もう“来ましたか。」. I tend to use 「まだ来てない」.