I’m wondering if it’s pseudo religious with humans being created in God’s image (Ancient Aliens stuff), the human-centric idea that intelligent life must resemble us, it being easy to make costumes for movies and TV when all you need to do is paint someone’s skin, or if SciFi writers were going for the uncanny valley effect for example.
If you’re asking why it appears in our sci-fi, you were correct in assuming it was mostly about cheap costuming and special effects. If you’re asking for a general canonical reason for it, there isn’t one, but many sci-fi shows have come up with unique ones (for example, Star Trek had the Progenitors, a species of humanoids that seeded world with their DNA). If you’re looking for a possible real-world explanation that could account for it, Convergent Evolution might explain why intelligent species wind up being bipedal tetrapods.