If you open a page with Magic Window content in VRShell it receives poses and renders correctly (although the motion is a bit awkward relative to your head). When entering WebXR and exiting back to VRShell, however, the Magic window poses stop being delivered, leaving the page to render without any view matrices. (This typically shows up as the page simply rendering the WebGL clear color.)

Exiting VRShell or refreshing the page makes Magic Window tracking resume again.

Magic Window tracking should work consistently no matter how you arrived at the page.