The blink program drove one pin with two #defines and it was the right amount of code for one pin. The second pin costs another two, the first alternate-function pin costs four, and by the tenth you have shift arithmetic scattered across the codebase with the pin number written out by hand in each place. The fix is not a HAL. It is about eighty lines that name what the hardware already does.
"Bare metal" does not have to mean "type every address yourself". Between raw pointer casts and a full vendor framework there are three or four distinct layers, each with a different bargain, and the useful skill is knowing which one you are standing on and why — not picking a side.
Out of reset the STM32F411RE runs at 16 MHz on an internal RC oscillator, which is a deliberately conservative choice: it works with no crystal, no configuration, and no risk. It is also one sixth of what the part can do, it is accurate to about ±1 % over temperature rather than the ±20 ppm a crystal gives, and it cannot produce the 48 MHz that USB requires. Somewhere in the first week of a real project you will need to change it.
A peripheral is a piece of digital logic sitting on the same bus as your RAM. It has no API, no calling convention and no way to be invoked. The only interface it exposes is a small block of addresses: write a word to one of them and some flip-flops change state; read from another and you get the current state of some wires. That is the whole model.
volatile has a reputation for being either a magic word that makes hardware access work or a deprecated relic that nobody should use. Both readings come from the same place: people learn what it does by observing that adding it fixed a bug, and never learn the boundary of the guarantee. The boundary is narrow, it is written down precisely in the C standard, and knowing exactly where it stops is what separates code that works from code that works on your desk.
Blinking an LED from an Arduino sketch takes two lines and teaches nothing about the machine. Blinking one with no HAL, no IDE and no library takes about ninety lines spread over five files, and by the end you know where every byte of the image came from, what the processor did before your first instruction, and which two writes in the whole program actually made the light change.