When adding a website as a web app, the resulting 'app' will have broken extension support.
Installed extensions either don't work (as if never installed) or are broken.
As an example, "ScrollMaps" (from Google Chrome, an extension to let you use the touchpad in a way that is intuitive on Google Maps) just does not work.
Meanwhile, Bitwarden (Chrome ver.) once showed the autofill icon, however pressing it (which would usually prompt you to unlock your passwords) just opened a small blank window (I have since been unable to recreate this, and the icon just does not show).
Additionally, integration with Apple's proprietary 'Passwords' app seems to have been turned back on, despite being disabled everywhere else: 
Extensions should work in web-app-windows the same as they do in normal browser windows.
macOS 15.5 (24F74) & Orion version 0.99.134-beta (WebKit 622.1.9.19.2)
Sequoia (15)