THey understood it?
Why did they have to "understand it"?
It was explicitly communicated to them. The anti-federalists argued that the the States should remain sovereign. The federalists argued against it.
The Federalists won. With the Constitution largely written by the nation's leading Federalist, in accordance with the Federalist Papers. With a thorough majority of the founders supporting the Federalist vision.
Worse for your argument, in NY, Antifederalist John Lansing Jr tried to put language into their ratification of the Constitution that would grant them the authority to secede if they chose. Madison shut them down, declaring in a letter read by Hamilton to the NY ratification representatives that the the constitution must be adopted in toto and for ever. And that Congress would not consider a conditional ratification to be valid.
Here's the letter:
First, Hamilton's question regarding 'receding', or leaving the union.
Alexander Hamilton in a letter to James Madison said:
"You will understand that the only qualification will be the reservation of a right to recede, in case our amendments have not been decided upon, in one of the modes pointed out by the Constitution, within a certain number of years, perhaps five or seven. If this can, in the first instance, be admitted as a ratification, I do not fear any further consequences. Congress will, I presume, recommend certain amendments to render the structure of the Government more secure. This will satisfy the more considerate and honest opposers of the Constitution, and with the aid of them will break up the party.
The Right of Secession. - NYTimes.com
And now the relevant portion of Madison's reply, which didn't contained the slightest ambiguity:
James Madison on the issue of the right of secession said:
My opinion is that a reservation of a right to withdraw, if amendments be not decided on under the form of the Constitution within a certain time, is a conditional ratification: that it does not make New-York a member of the new Union, and consequently that she should not be received on that plan. Compacts must be reciprocal; this principle would not in such case be preserved. The Constitution requires an adoption in toto and FOREVER. It has been so adopted by the other States. An adoption for a limited time would be as defective as an adoption of some of the articles only. In short, any condition whatever must vitiate the ratification.
Madison's letter was read publicly. Lansing's secessionist language was removed. And NY ratified the constitution.
This wasn't a grand secret. This was thoroughly understood, debated, and discussed at the time. The Anti-Federalists took your position. The Federalists, Madison's.
The Federalists won.