My experience is that this seems to be pasteboard driven problem. Play with the H and V pasteboard dimensions in the preferences and you'll see what I mean. Try two small settings of 10 or 20 for example, and then view the doc at 100%, wiggle something around so you can save the current view setting, close and reopen. It should open very close to your last saved view. Now try the same with larger pasteboard H and V sizes - try 1000 each. Now, for me anyway, the document is being pushed down and to the right of its last saved view setting. It seems the upper left limit of the pasteboard determines the degree that the opening document is offset down and to the right when opened. This makes it seem that ID's fixation on that upper left pasteboard corner is carried into the last saved view coordinates when the doc is saved and closed.
I would think ID would fixate on the center of the pasteboard regardless of H and V amounts. (?)
Hopefully, you can tweak out a workable solution by altering the H and V amounts.
iMac 27-2012: 3.2 GHz i5
I verify that there is an inconsistency issue in saving/reopening an InDesign document with a custom view. It's not something I encounter as I use InDesign, possibly as I generally save with zoom level set to Fit Page/Spread in Window.
I wonder if this issue is more apparent on Retina/hiDPI displays then on standard displays. Would be interesting to know.
I tested on Retina display just now.
If you want to submit as a bug to be fixed: Adobe InDesign Feedback
Thank you and yes, Fit Page/Spread seems to be the best way to alleviate the situation. The only time the pasteboard settings made a difference to me seems to have been when I wanted the document to open at 100% or smaller and be centered upon opening. This could be explored much more thoroughly than I attempted and that was part of the motivation in posting.