This is more a limitation rather than a bug.
To speed up the process, the tool uses the incremental updates schema, where changes are appended to the end of the pdf document file, not messing with the complex PDF file structure.
This has advantages, but also the inconvenient you refer. PDF readers can't consider anymore a PDF document, as optimized for Fast Web View, after an incremental update section has been added to the file.
In my opinion this is not completely true, the reader could easily integrate the incremental updated sections when tasking to show first document page, but only the reader developer can decide if its reader support this functionality, and Acrobat don't has this capability.
I intend to develop into a further new version release an PDF optimizer tool, and the optimize for Fast Web View will, for sure, be one of the optimize options. Meanwhile, if you want to use PDF-ShellTools, and get/maintain the file optimized, you will need to use a third part PDF optimizer after imposing the open options.