Served in the Navy and was stationed in Japan for three years.

It is not inaccurate.

TLDR: The U.S. is not taking over Japanese assets and under any circumstances barring alien invasion and kaiju. (In the case of kaiju, we should probably operate under Japanese control.)

While we practice/train with the JMSDF, and have ok interoperability, there is zero infrastructure for us to control them.

It would actually hurt us and would be easier to tell them to stay home while we did everything than to try and control both assets at the same time.

However, we can work together, by assigning each service their own responsibilities and let each perform those responsibilities within their own chain of command. That would work peachy.

In that sense, we may have overall strategic command, but the Japanese would absolutely have a seat at the strategic table, and the Japanese would and should take their toys and go home, the minute we asked them to do something against their best interest.