Is the Endeavor's supercollider the only way to have equipment overclocked?

No! Chris outlined his plans for a robust overclocking system early in the game, in the hopes that players will eventually make careers out of being 'overclocking' experts capable of providing the best tuned weapons and other components. While we see the Endeavor's supercollider (name change pending, re: science!) as the ultimate tool for this task, the climb to that level will start with the already-offered workbench.