Currently, only the window settings (i.e. window size) of forms is persistent in
database documents.

However, in real-life databases, I often have different queries showing
different aspects of the database, and work with those queries instead of
full-blown forms.

Unfortunately, for queries (and, for that matter, also for tables) the window
settings are not persistent: If I open a query, adjust the window size so that
it optimally fits the content, close and re-open it, the layout changes I just
made are all gone.

I suggest that the window size is remembered on a per-object basis, for all
objects - tables, queries, forms, reports - in a database. Additionally, I
suggest that for all objects those objects the settings are remembered
separately for different modes. That is, if I design a query, I probably want to
have another window size than when I view the data resulting from the query.