The Bible-Boooooring

[Neo-Scholastic]

Not necessarily so. The existence of a soul is not a 'God in the gaps' explanation. It is a theory to explain all observed phenomena.

...when that phenomena can be explained through a natural explanation, why is it that people will deny that and continue with their soul theory?

You seem to be creating two catagories: natural processes and supernatural processes. Then you treat both as intermediate causes within a chain of events, like this: natural cause A has supernatural effect B and that supernatural effect B becomes the cause of a natural effect C, and so on. That would be a 'God in the gaps' type of theory.

A soul would not serve as a bridge between two natural causes in that way. Efficient causes can go directly from physical cause to physical effect without any intermediary. What the soul would do is this. It would constrain what is possible within any causal chain and provide an ontological basis for immaterial attributes (like qualia and meanings) that correspond with natural processes.