I do also boot with the original bitstream and replace with my own at runtime. However, simply loading the bitstream won't change your FCLKs, you need to do it explicitly before replacing the bitstream with your own (like the thread you reference mentions).
To achieve what you want, I would also ask over at Xilinx forums as this is not a question specific to Parallella.
But if I were you, I would simply write a script that executed as soon as Linux finishes booting and replaces the original bitstream with your own and changes clocks accordingly. From what I gather, you would obtain equivalent functionality
