### Godot version

v4.2.dev.custom_build [60f3b7967]

### System information

Debian Linux X11 Xfce

### Issue description

Physics Picking within a `SubViewport` happens with `InputEventMouse` even when mouse events are disabled via `SubViewportContainer.mouse_filter = Control.MOUSE_FILTER_IGNORE`

The problem is that passive hovering still happens in the `SubViewport` with `SubViewportContainer.mouse_filter = Control.MOUSE_FILTER_IGNORE`.

I assume that it is a regression from #78017.

This was initially reported as a side-effect in #79271, which got closed, because the main issue was resolved.



### Steps to reproduce

1. Load and run MRP
2. move mouse over Icon

I would expect, that the `Area2D` receives no `InputEventMouse`, however it gets `_input_event` and also mouse-entered and mouse-exited signals.

### Minimal reproduction project

[IgnorePassiveHover.zip](https://github.com/godotengine/godot/files/12044510/IgnorePassiveHover.zip)

set_positional_shadow_atlas_quadrant_subdiv(1, SHADOW_ATLAS_QUADRANT_SUBDIV_4);
	set_positional_shadow_atlas_quadrant_subdiv(2, SHADOW_ATLAS_QUADRANT_SUBDIV_16);
	set_positional_shadow_atlas_quadrant_subdiv(3, SHADOW_ATLAS_QUADRANT_SUBDIV_64);
	set_mesh_lod_threshold(mesh_lod_threshold);
	String id = itos(get_instance_id());
	input_group = "_vp_input" + id;
	gui_input_group = "_vp_gui_input" + id;
	unhandled_input_group = "_vp_unhandled_input" + id;
	shortcut_input_group = "_vp_shortcut_input" + id;
	unhandled_key_input_group = "_vp_unhandled_key_input" + id;
	// Window tooltip.
	gui.tooltip_delay = GLOBAL_DEF(PropertyInfo(Variant::FLOAT, "gui/timers/tooltip_delay_sec", PROPERTY_HINT_RANGE, "0,5,0.01,or_greater"), 0.5);
#ifndef _3D_DISABLED
	set_scaling_3d_mode((Viewport::Scaling3DMode)(int)GLOBAL_GET("rendering/scaling_3d/mode"));
	set_scaling_3d_scale(GLOBAL_GET("rendering/scaling_3d/scale"));
	set_fsr_sharpness((float)GLOBAL_GET("rendering/scaling_3d/fsr_sharpness"));
	set_texture_mipmap_bias((float)GLOBAL_GET("rendering/textures/default_filters/texture_mipmap_bias"));
#endif 
	set_sdf_oversize(sdf_oversize); // Set to server.
}
Viewport::~Viewport() {
	// Erase itself from viewport textures.
	for (ViewportTexture *E : viewport_textures) {
		E->vp = nullptr;
	}
	ERR_FAIL_NULL(RenderingServer::get_singleton());
	RenderingServer::get_singleton()->free(viewport);
}
//
void SubViewport::set_size(const Size2i &p_size) {