Agreed. The Bielsa case amounted to the exploitation of a regulatory loophole whereas the FA will consider Eckert's case a deliberate violation of rules put in place by the EFL.
Also, the perceived severity of the EFL punishment on the club will be immaterial to the FA's personal charges against Eckert. Any collateral damage caused by the fallout will likely be considered irrelevant by the KC and two football "experts" chosen to decide a punishment. You can be pretty sure the FA will put forward the case that a severe precedent should be set.