The program written in C and compiled on some other IDE/computer (or cross-compiling) and then loaded as binary data into the flash memory of the controller.
What am i not understanding in Bare Metal / No RTOS
Ideally your program runs in flash not ram. Many mcus you can, it would be an architecture limit primarily if running from ram is not supported. In a pinch you can run your code in ram if you need a trampoline to reprogram the flash as in downloading new firmware in the field (for a chip with only one flash bank that can't run and be erased/modified at the same time), or for performance, but if you need ram for performance then perhaps you need to rethink your design. small sections sure, but if the whole app has to be in ram for reasons other than development, you need to re-think your system design.
You can easily wrap your program with a small copy to ram bit of code, so that the mcu boots up the copy and jump program and then the main application runs in ram. that is your choice. somewhat trivial just a few lines of code. it is chip/architecture dependent on whether you can handle interrupts in that situation or how you need to design it (more than just a copy and jump for example, might need handlers in flash that hop over to ram too).
There is no magic here, the mcu processor is no different than others you need some non-volatile way to get the program in there. Like most others cpus your processor boots from a rom/flash, then as desired it works toward the final application be it an operating system or not. for an mcu the typical approach is to boot right into the application, run the application in flash for read only items (.text and .rodata) and the read-write in ram (.data, .bss) which is handled by knowing how to use your toolchain, which is a critical part of bare-metal success.
CPUs generally don't care about flash, ram, peripherals, they are just addresses, the cpu is very very dumb. You the programmer are smart you lay the tracks down for the cpu to follow, the instructions have to follow the rules and guide the processor. The processor starts in a well known way at a well known address or vector table, from there it is all on you to keep the processor on track by working within the address space where there are resources, flash, ram and peripherals. The processor may have rules on the address space it can fetch/execute from, or not, depends on the implementation. For implementations where the executable address space has both flash and ram then yes you can simply place code in ram and execute it.
Running code in ram on an mcu is the exception not the rule.