There are many ways for an application to overwrite a file, different API's with different side effects.
As a former developer, I'm well aware of the APIs. However, you don't actually think that Adobe managed to find APIs that nobody else is using, in any other software that either of us has tried, including other Adobe products, do you? That does not make sense at all.
The fact that Activity Monitor reports the file as being open does not mean anything, since that fact does not affect me in any way at all, nor does it affect you in any way
except when doing one specific thing in InDesign. We do not know what Activity Monitor is actually reporting, how often that list of open files is refreshed and many other things.
What you have demonstrated thus far is a problem with InDesign. Most likely, knowing Adobe, they have misused the APIs by relying on undocumented behavior or they are still using deprecated APIs somewhere in the InDesign code. This should be reported to Adobe.