It seems to me that the specification could use an identifier in the head of the document in order to use the features, just as xhtml in ePub books uses an identifier to advertise that it might use custom ePub tags indicating the document structure.
Valid ePub 3 head for a book using structure for assistive readers
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:epub="http://www.idpf.org/2007/ops"
An application should require metadata that activates the extra read/write features as menu items in the browser.
<html xmlns="http://www.w3.org/1999/xhtml" xmlns:webapp="http://www.w3.org/2018/webapp"
A non-verified browser would ignore the special tags in the webapp scope or could display a dialogue to ask permission to open the page in a compliant safe browser.
Only allow web apps that are strictly XML compliant and that do not include inline
<script> elements. Like XHTML, the browser should display an “error on line nnn” message if the page is not compliant with the webapp specification.
Consider specifying an alternative “chrome” (appearance) for web apps, like incognito mode does, to remind the user that the page can read and write files.
Consider W3C accessibility standards. For example, can you access the
Save As... commands with no mouse using a keyboard shortcut or tabbing to a button?
Allow the user to quit the application (CONTROL + Q) even while an alert or menu is showing without having to resort to a system-wide process manager.
Where do the commands appear, in the browser window or in the “File” menu in the browser chrome?