In Presser the court did not rely on the 2nd Amendment's militia clause for it's declaration that a state could not deny it's citizens the RKBA. It only referenced the militia to show that the federal government has a vested interest in an armed militia in as much as the militia is the body of men from which the federal government obtains troops for it's armed forces.
In any event, it is still true that the cited portion of the Presser decision says that a state can't enact a law which denies it's citizens the RKBA, and that the restriction on the states is based on the federal government's power to raise it's armed forces from the body of citizens which comprise the militia.
The state cannot prohibit the people from keeping and bearing arms so as to deprive the United States of their power to call forth the Militia. The state could insist that citizen's arms be kept in the state armory. The state could supply arms to be used in training.
Keep in mind that the federal government has the power to "provide for organizing, arming, and disciplining the Militia".