Unfortunately in reality you often can't just expect code to be conjured out of thin air, you have to be able to code, and frankly walk other code to understand how it works and interacts. This doesn't have to go into the minutia, unless necessary, but you need to get an overview / lay-of-the-land, so you know where to look when that becomes necessary.
Cube hides stuff all over the place, the Semtech LoRa stuff less so, and in a less transparent way, you'll see it call specific tasks to do specific things. Look in the "HW" files, rather than "MSP" files.
Would suggest investing some time/money in Static Analysis tools so you can navigate code, and understand the inter-play. Within your chosen IDE, look at the Right-Click type context options to follow code, calls, definitions, etc, look at the Find-in-Files type searches, and perhaps in a File Manager so you can navigate code trees, and find things that way too.
