Hey, I have seen your progress.
I tested a single component (Popup) with treeshaking.
First of all, there is a need to use the Leaflet.js as the entry file LeafletWithGlobals registers the modules directly which does not really make sense. see #9880

The problem with Popup is still the static part with this.setDefaultOptions which is a side effect. I found an experimental option in rollup: experimentalLogSideEffects: true.
This logs the first sideEffect of every file and could help to identify the problems.
I proposed to use mixins or some kind of plugin system in #9814, in my opinion it could be a little bit overkill to add mixins to all the control and map handlers as they are used anyway (Control.Layers is a good example for the usage of mixins as it is a rather big file and is not always used). In control/index.js these components are used anyway:

Control.Layers = Layers;
Control.Zoom = Zoom;
Control.Scale = Scale;
Control.Attribution = Attribution;

but the components are registered in LeafletWithGlobals which increases the complexity without any benefit (at the moment as they are not treeshakeable yet). Primarily, this means that the shortcut Control.* shouldn't be available anymore (or add it in the register function if possible).

static register() {
    Control.Layers = Layers
    ....
}

Let me know if I can assist you in any way.