In Managunz or wMM, to apply underclocks & overclocks semi permanently (until a new pup installation) with any valid combination of core/memory settings, one could write new code to extract CoreOS from Flash Memory, decrypt/unsign lv1.self, patch the elf, reencrypt/resign it, if ever the self file size is bigger, rebuild CoreOS & finally overwrite CoreOS in Flash Memory, with a post write hash validation check for good measure.
Applying overclocks/underclocks on the fly at runtime is more complicated, like ze mentioned before, restarting lv1 without reinitializing the entire memory and reloading the self from Flash Memory, consequently losing under/overclock patches, must be feasible but it would probably require one or more lv1 patches to be determined.