Separation of powers ended in 1947 with the creation of the NSA/CIA, which are under executive control with no congressional oversight and frankly untouchable legally. While there were several important issues the FFs missed (intentionally imo), there was no way they could envision the national security state.
Your post is sadly correct. Aside from that, the distortion of the commerce clause, into a tool that allows the federal gubment to regulate anything and everything because anything might impact interstate commerce has been an utter disaster. the combination of the proto-communist national security state plus the precedent of letting the fed regulate everything has been a disaster for freedom and prosperit.
Pursuant to the Agricultural Marketing Agreement Act of 1937, conferring on the Secretary of Agriculture the power to regulate the handling of milk which is "in the current of interstate or foreign commerce, or which directly burdens, obstructs or affects interstate or foreign commerce in such commodity or product thereof," the secretary issued marketing orders fixing minimum prices to be paid to producers of milk in the Chicago area. Respondent, who purchased and sold milk only within the state of Illinois, refused to comply with the order. The United States sought enforcement of the order, but the complaint was dismissed. Held, reversed and remanded. Congress has the power under the commerce clause to regulate intrastate transactions which affect interstate commerce even though this effect is caused only by competition, and such power was conferred upon the Secretary of Agriculture by the act. United States v. Wrightwood Dairy Co., (U. S. 1942) 62 S. Ct. 523.
some would say it ended March 27, 1861 when Congress adjourned sine die when seven southern states walked out preventing a quorum
others would say it ended April 15, 1861 [peculiar day, no?] when President Lincoln reconvened Congress under the Executive branch by proclaming
"I do hereby, in virtue of the power in me vested by the Constitution, convene both Houses of Congress."
This effectively [re]organized both houses under the executive branch and creating an executive run administrative democracy, little d and not a republic.
The Constitution does allow for concurrent parrallel forms of governent and judicial systems which were originally intended for governing and servicing territories, etc.
Maybe FF didn't envision Federal territorial [district] overlays that would offer a 'choice' between Federal government originally limited to the [Federal] District of Columbia or local goverment in the form of an independent Republican state or commonwealth. Maybe they did.
What is the Ninth Federal District?
I have previously brought up the Lieber code [General Orders 100] ordered by Lincoln, and never rescinded, which describes how belligerents in the field are to be managed in the territories otherwise known as Federal districts.
Just realize that a belligerent is anyone that may find Federal district rule to be repugnant. And so, the Feds treat everyone a belligerent until proven different or they can get you under an oath of office [under penalty of perjury, a crime violating an oath of office (sound familiar?)] or strict administrative control [prison].
Think of the Lieber Code as the original Patriot Act.
There is reason why Federally organized state run schools refuse to teach belligerants history and English comprehension.
Election Day at Bernies