original Playstation used similar copy protection trick - ASCII string SCE(I/E/A) was stored in pregap pre-groove wobble between the leadin and the first track. PSX used Three-beam pickup and was able to track this wobble and extract code from radial tracking error signals. Modchips simply injected same error signal for couple of seconds after closing CD lid, enough for the CD controller to recognize it as "original".
they didnt. lasers were poor to begin with, plus weaker media(cdr) probably caused extra mechanism movements (focusing)
edit:
hmm, now that I think about it, its possible someone incompetent made modchip that would keep sending wooble constantly, that could cause tracking problems and tire mechanism pretty fast.