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When using sqlite3_step(stmt) inside a transaction my busy-handler is not being called
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> my condition is a simple stand-alone application that does not share the database with other applications

What SQLite cares about is that there are multiple connections.

> Is there a way to configure sqlite to always call my busy-handler callback?

And what would your busy handler do? In case of a deadlock, waiting would not help.

> I found that when using IMMEDIATE transaction my callback is being called and all seems to work, but I am not sure on how solid this solution is

A deadlock happens when two read-only transactions want to upgrade to read/write. BEGIN IMMEDIATE starts the transaction as read/write.