It's kind of hard to follow this stream of conscious, but here a few facts which hopefully can answer some questions:
1. FPGA can be configured in many different ways, they typically have strap options to specify which configuration method to use. These straps are typically read during FPGA initialization, in some cases for a change in this strap config to take effect, one would require a power cycle FPGA.
2. SPI/QSPI is the popular one because QSPI flash chips are readily available, cheap, doesn't not require many pins and is very easy to implement. Some FPGA vendors implemented a way to program such memory devices in-system through JTAG, which is very handy for quick iterations.
3. Some FPGAs allow reusing remaining space in a QSPI memory device for application use, this allows consolidating both FPGA bitstream and firmware for a softcore inside a single memory device.
4. As (1) notes there are many ways to configure FPGA, QSPI flash is by far the most popular, but there are more, including using BPI (parallel flash), JTAG, some custom serial or parallel protocols which can be used by a dedicated CPU/MCU to configure FPGA from software, some FPGAs can even re-configure themselves dynamically.