PWA is intended to be app-like so some browser specific things ("hide header", "progress type", "keybinds" + others) will be disabled or omitted due to layout differences between web/PWA reader.
If you prefer to have progress always visible, the "show page number when progress is hidden" option will keep both the progress bar and page number visible (the progress bar will be minified and transparent as shown below).
There are currently no plans to add more customization to the PWA progress bar. If you REALLY do not like it, your only option as of now would to be use it in browser and not as a PWA.