The JTAG/SWD operates via a different method, it uses internal scan-chains within the IC to access processor registers, indirectly accessing buses, peripherals and memory. It gets into the internal workings of the chip, and is a rather deep rabbit hole. The ARM docs might be the best to understand the mechanics there.
Typically factory programming is done via JTAG/SWD, as well as debugging. The boundary scan offered by JTAG would allow for pins and circuit nodes to be tested.
The System Loader in ROM also provides alternate means, using serial for example is a cheap and scalable method. Review AN2606 to get an overview of the pins involved on specific parts. Writing SW to interact with UART is something a developer should be able to do on their platform, ie Windows, Linux, MCU
Should consider exposing SWDIO, SWCLK, SWO, NRST, GND as test points, headers, or edge castellations so you can readily fixture and program. A serial port you can commit for debug telemetry and/or UART programming are also helpful. Pull BOOT0 down, but allow for the pin to be driven high by pin/test point.
If you already have a USB or UART/RS232 interface use those as means to program.
Avoid attaching GPS/GNSS devices to the UARTs that the loader checks, these will squawk at startup and confuse the loader. For STM32 that allow for RX/TX reversal, you could use that to avoid triggering the loader with such signaling.
