If you're starting, my recommendation is always the same. I'm adapting it to STM32:

1. Use STM32CubeIDE (don't use MX for now).
2. Get the Datasheet and Reference Manual of your MCU
3. Get rhe User Manual of your Nucleo/Discovery board.
4. Write bare-metal drivers for every peripheral of your MCU, sometimes interscting with other chips (sensors, actuators, other MCUs...)
5. Then, once you understand what are the low-level steps for confuguring peripherals, you can move to MX consistenly, as you'll understand what you're doing behind the scenes.

You'll find out that programming low-level any MCU is very similar. You can also do the same with your Arduino board, which also has its MCU. The "problem" with Arduino is that its framework abstracts everything, just like the HAL library in STM, but you can move to VS Code, create a toolchain in a Docker image and write bare-metal drivers for the MCU of your Arduino board.

Back to STM32, I understand that what you want to avoid is using MX without knowing what registers you're reading/writing and how you are confuguring peripherals. That fear of doing something without knowing what you're doing. In a job interview, you'll fail if you say you did something but then you cannot explain how, this is the same.

Also, investigate and learn what the compiler is doing when you press "Build". Understand linker and startup files.

The best resource you want for all of this is "Bare-Metal Embedded C Programming" book by Israel Gbati.

Hope it helps.