The federal government has no police or enforcement power or authority over the numerous city-states, such as the Greater San Francisco-Oakland Bay Area, or the Chicago Standard Metropolitan Statistical Area, except as specified in the Constitution and as itemized by Scotus. If a county clerk is for instance in violation of the Constitution, the federal courts with their U.S. Marshals can and did intervene. Likewise, if a fascist might be denied free speech, the federal government can and has intervened -- but almost exclusively in instances where local or state authorities have failed in one way or the other.
However, absent specific federal authority as provided in the Constitution and in the laws, the federal government has always yielded to the authority of the state over matters of crime and civil law. An exception would be when the feds are requested by the state authority, or perhaps the local authority via the state government. This has been the rule, unless Potus declares a State of Emergency to exist in the place based on national security -- and predicated in the law and the Constitution.
Given Donald Trump knows nothing about SMSA, state vs federal authority, the Constitution or the laws pertaining to civil disturbance or having to do with the public safety or welfare, he'd need to stay out of matters such as the riot at UC Berkeley among the others you vaguely reference. The Berkeley situation was handled comparatively well by local and state authorities who exhibited a model of excellent horse sense and judgement. The feds from Washington would have only mucked it up -- severely and predictably.
Further, we would indeed have a Constitutional Crisis if the governor of a state activated the National Guard which he/she commands but then the Commander in Chief in the White House federalized it, as he has the absolute authority to do, but then again the National Guard of the particular state declined the order of the CinC to instead remain under the sole command of its governor who is its original commander (dating back since colonial times). Or if a significant part of the state's National Guard did this or anything like it. We should be cautious not to invite any such scenario(s) in any particular or given sovereign state. This is the case whether it be the state's official National Guard militia, or its semi-military law enforcement personnel at the local, county or state level respectively or inclusively.