You are right it is an outlier and some would say not ideal. It is transparently a breakdown of rule of law into realpolitik given constraints and the redundant levels of powers - from what is fundamentally bad law and consistent failure to respond to facts on the ground. It brings to mind the old bit of legal philosophy about unenforceable laws breeding contempt for the law in general.
The Federal government can technically roll up and enforce the laws federally at any location they please but they don't have the budget or manpower for it. Unfunded mandates can't be enforced upon the lower levels of enforcement and they depend upon them for cooperation. They could technically have thrown the bulk of their enforcement budget into an early adopter but that would be playing whack-a-mole as others could crop up and openly defy them while they are busy there - all while 49 other states are complaining about there being way better uses of their resources than replacing every vice squad in California.
The federal government caused the problem in the first place in their adamant refusal to acknowledge reality with Schedule 1 classification - not just in assigning it to marijuana which trivially has medical uses but in that the very category is a tautology. We don't know if something has medicinal use until we try it in every application. For all we know even something horrific like krododil may be very good chemotherapy for treating specific kinds of tumors. Weaning off of heroin may well be the best approach to beating addiction - it is already accepted for nicotine in general practice! The specifics don't matter so much as the general point that Schedule 1's very existence is an outright tautology and illogical dogma.
They could have avoided the massive backlash and much of legalization movement's momentum being a serious thing by making Marijuana schedule 2. This isn't even something radical, not even decades ago - you have been able to find cocaine in ENT applications throughout the country perfectly legally given that there really is no better substance despite the known downsides.
The whole thing is fundamentally a failure state on the law. It is technically a solution in that it prevents enforcement of bad laws but it really highlights the systemic dysfunction and creates greater inconsistency. It is a matter of debate if being able to have this is a good thing or not.
I can think of one similar issue as well however that is even lower. The Sanctuary City "issue" (an emergent solution that some don't like) is a similar disconnect of high-level dogma colliding with and failing to respond to low-level reality - any significant urban police force knows they would have to be extremely stupid to have a zero-tolerance deportation policy when they depend upon the population for witnesses and crime reporting. It is beyond a matter of even demagogic politics locally while many above consider its state unacceptable.
TL;DR version - the law refused to bend so it broke instead.