The problem is you are influenced by 2,000 years of an unbiblical philosophy known as DDS (Doctrine of Divine Simplicity) that distinguishes the physical from the spiritual based on Plato's fairytales regarding the existence of so-called "immaterial substance" (complete nonsense). In the biblical metaphysics, all substances including God are physical. See my thread for exegetical proof:
God Is a Physical Being
Since God is not a fan of ceremonies/rituals such as water baptism, He only institutes them where He plans to show up on the scene for real, palpable interaction with His Presence. And we can't just assume this is occurring with today's water baptism - just because He authorized it for the early apostles doesn't mean it's still authorized right now. Authorization is an epistemological issue so, instead of getting side-tracked on that clarification, I'll get right to the point. Which is this.
When the apostles dipped people in water - since it was an
authorized ceremony - the Third Person showed up palpably, as physical Living Water, either by replacing some of the existing water, or by permeating it. As a result, water baptism served as a further cleansing, an incremental sanctification, in the early church, literally washing away the sins of men.
Howard Ervin's term for such physical modalities of the divine Word is "sacramentalism" (such as "sacramental baptism"). In Catholic theology, it is called the Real Presence. And there are many biblical references to it, for example at the last supper when Jesus said, "Take this bread, and eat it, this is my body." Or again, "Unless you eat my flesh and drink my blood, you have no life in you."
Notably, even James Dunn, in his famous dispute with Howard Ervin on sacramentalism, found himself forced to admit that Romans 6:3-4 - based on grammatical/contextual analysis - provides a solid exegetical basis for concluding that water baptism washes away sin. This was an amazing, startling concession since Dunn himself does not take this stance and was doing everything in his power to refute it.