Jefferson used the term in the Declaration. I've seen subtantial discussion about the meaning of inalienability in the philosophy journals about just the conflict you describe, but it seems clear to
me: Certain rights are granted to each "
by their creator", or if you like they are yours by virtue of being human. The fact that someone might deprive you of their agency by force does not make them any less inalienable. Later Jefferson goes on to add the practicality: "
to secure these rights, government are instituted among men." - some government, not necessarily the federal government.
Rather than try to iron out the legal details of your points about conflicts in the constitution, I'll draw your attention to some familiar US history. The Declaration conjured up no central government. We find no great cry for additional protection of the rights of individual after the revolution and prior to the Constitution. The thirteen state governments were already in existence to protect the rights of the individual, many of them already having their own bill of rights. The impatience at the time was with the flawed cooperation between the states, not with any need to protect individuals, and this was the reason for the creation of the federal government. Ten years or so after the revolution, the states grudgingly draw up a federal government to fix foreign policy, raise an army and navy, run the post office, and settle disputes between the states with a court system. That's about it. As Madison expressed at the time the concern about the ability to control the government they were creating:
the great difficulty lies in this: you must first enable the government to control the governed; and in the next place oblige it to control itself.
It is clear to me that the enumeration of powers, and all the of the ten amendments were put there to control that government. The central government was needed only to do things of national scope,
not because the people needed it to protect their individual rights. That's my take.