HPS vs FPGA configuration

No indeed, the options you set in QSys for the DRAM and other HPS parameters aren't actually compiled in the FPGA image, but are used when you generate the preloader. It is the preloader that will configure the HPS part. Just remember to regenerate and reflash the preloader each time you change those parameters.

The default HPS mode is set with the dedicated pins (clock select, boot select, and maybe other ones, I don't remember) and this default mode is just enough to load the preloader into the internal SRAM and start it.