As a result of Lincoln's successful interpretation and FDR's solidification into law, it has become "commonly held", although I wouldn't think the American people would support such absolute power in one person, even though they have done exactly that by their silence and complicity...
Note also that the Militia Act of 1795 leaves when to call out the militia to the judgement of the president.
So, is that the answer to my question "Does that give him carte blanche to discard individual's and state's rights as well"?
Clearly, the answer is NO. No man is a law unto himself - that's why we have the U.S. Consitution. It is superior in force to ANY man.