You make the States sound like some sort of political Barcalounger -- a convenient thing to have around, until you trip over it. They are a lot more than that, but then amalgamators like you and Non-Sequitur have never had any use for States anyway, as N-S posted above. They are an impediment to a Phalangist exercise of unlimited and illimitable federal power, so you derogate them despite their historical and substantive presence.
If King Charles chartered separate colonies under the British Crown are they forever to be sovereign with no ability to form a more general government?
Red herring. Of course they did. They did not, however, as you so fervently wish they had, annihilate themselves when they formed the Union.
...the Constitution is more than a mere league of independent states.
Of course it is. But Madison meant what he said in Federalist 45, quoted above, when he said that "[t]he State governments may be regarded as constituent and essential parts of the federal government; whilst the latter is nowise essential to the operation or organization of the former."
The States are the organic entities of common interest and allegiance that preexisted the Union of the Constitution, and it was to the People of those States that the Framers had recourse, when they sought the People's assent to form the new Union.
But it looks like you're willing to fight over the word "sovereignty." One problem is that the states relinquished most of the attributes of sovereignty at the beginning of the Republic -- separate armies, navies, currencies, embassies, treaty-making, import regulations, etc.
One point I'll "fight" about is your use of the word "relinquish". They delegated and foreswore for themselves the exercise of certain enumerated powers (and, Marshall insisted later, certain ancillary ones -- and, Franklin Roosevelt insisted much later, the power to weigh pigs and produce!), but they didn't alienate them forever. Rather, as everyone from Hamilton to Madison to young John Marshall understood at the time, powers not granted to the new Union remained with the States and their People. Thus Marshall, in 1788:
The state governments did not derive their powers from the general government; but each government derived its powers from the people, and each was to act according to the powers given it. Would any gentleman deny this? He demanded if powers not given were retained by implication. Could any man say so? Could any man say that this power was not retained by the states, as they had not given it away? For, says he, does not a power remain till it is given away?
-- Elliot's Debates, Vol. III, p. 419
And here is Hamilton in Federalist 84, on the general subject of objections to the Constitution, addressing the topic of the Bill of Rights:
It is evident, therefore, that, according to their primitive signification, they [bills of rights] have no application to constitutions professedly founded upon the power of the people, and executed by their immediate representatives and servants. Here, in strictness, the people surrender nothing; and as they retain every thing they have no need of particular reservations ...bills of rights, in the sense and to the extent in which they are contended for, are not only unnecessary in the proposed Constitution, but would even be dangerous. They would contain various exceptions to powers not granted; and, on this very account, why declare that things shall not be done which there is no power to do?
And finally, the People of the United States did not give the federal government a threshhold or irrevocable grant of power, but a temporally durable, perpetually renewing trust of power that the People have the right and power to revoke at any time, and resume their powers intact. This is what the departing States did in 1861, whereupon they were set upon by Abraham Lincoln and his political machine, wielding the United States Army as their own instrument of revolution.
In the American Civil War, the revolution of secession was overreached by a coup d'etat of the servant against the master, and the whole American People lost both war and coup, not least the men of the Union Army who fought, they thought, to preserve the Union, but actually to end it.
The degree and kind of that loss would be expressed, over the coming century, in the progressive marginalization, trivialization, and demoralization of the American People, as what they had lost, or rather what the new ruling class had taken from them, began to sink in.
Once nominated to the court Marshall seems to have forgot what he stated during debates decades earlier. The Constitution itself notes that the powers were vested/delegated, not surrendered.