Facebook instant currently requires that games use canvases rather than webgl
As Godot currently only uses OpenGL ES for rendering (for 2D and 3D), it wouldn't make sense to use canvas rendering (which is less efficient, and only has very limited 3D capabilities which aren't hardware-accelerated).
They also require the game files to be around 1mb.
There is only so much that can be done to make a full-blown game engine smaller. (As you said, Unity suffers from the same problems when exported to HTML5.)
The WebAssembly module currently is around 3 MB when sent gzipped (which should be configured in the Web server you're using). If supported by your Web server, Brotli compression can help bring its size further down, but it would be unlikely to bring its size below 2.5 MB.
Disabling 3D support would help make it a bit smaller, but it would still be far above 1 MB when transferred.