Emscripten builds cannot create multiple windows because the code is written as if there will only be one canvas element in the document. I've looked into the code and believe these tasks needed to fix this issue:

• Remove Emscripten hints and make them properties Add create window properties to be overrides for hints(emscripten: move hints to window properties #12509 )
• Register callbacks that don't take an element as a parameter (i.e. emscripten_set_fullscreenchange_callback, emscripten_set_focus_callback, Emscripten_set_pointer_event_callbacks) during initialization. These callbacks should look through all of the canvases in the document and only handle the event for the focused canvas. (Emscripten: Move global event handlers #12738 )
• Update Emscripten_UpdateWindowFramebuffer to store multiple canvases and update the specified canvas based on the window_id of the window. This will only fix the software renderer. (Emscripten: Allow for Multiple Windows #12575 )
• Update Emscripten_GLES_MakeCurrent to update Module['canvas'] (Emscripten: Allow for Multiple Windows #12575 )