Fix some PyGObject deprecation warnings

like
The "flags" argument for dialog construction is deprecated. Please use initializer keywords: modal=True and/or destroy_with_parent=True.
or
Using positional arguments with the GObject constructor has been deprecated. Please specify keyword(s) for "title, transient_for, flags" or use a class specific constructor.

See: https://wiki.gnome.org/PyGObject/InitializerDeprecations