I don’t see that in any of them.
もしよければ、代わりましょうか
The object is omitted, but presumably it would be あなた marked by に, which would be intransitive.
王子は、けん玉に代わるあたらしいあそびを見つけた。
Here the object of 代わる is けん玉 and you can see that it’s an indirect object with the に marker.
私はスティーブ・ジョブズに代わる天才を探しています。
Again we have スティーブ・ジョブズに, an indirect object.
I take it when you said they are all transitive, you were talking about the English sentences? There need not be any relation between how a verb is translated and its transitivity in the original language.
The fact that “replace” is transitive doesn’t mean anything with regard to 代わる.
The verb 分かる is usually translated as “to understand” in English, a transitive verb. But 分かる is intransitive, and it doesn’t take a direct object.
How much Japanese grammar study have you done to this point? If what I’m saying doesn’t make much sense, it might make more after studying more grammar.