### Godot version

4.0 beta 11

### System information

Windows10

### Issue description

When setting GeometryInstance3D transparency parameter to a value higher than zero, mesh do not appear anymore if material transparency is not enabled.

 Worked fine in beta10 even if material was not set to transparent.

Not sure if it's a regression or a bug fix...


### Steps to reproduce

1. Add a MeshInstance3D with a Box shape
2. Change the transparency setting in GeometryInstance3D

Mesh disappears.

Beta 11 : 

![transp_bug](https://user-images.githubusercontent.com/3649998/211932790-15d92330-83dd-46f3-b975-6ecdcdb15984.gif)

Beta 10 : 

![transp_bugb10](https://user-images.githubusercontent.com/3649998/211932880-f94ad790-b982-4202-9514-abbdee3a2be0.gif)


### Minimal reproduction project

[transparency_bug.zip](https://github.com/godotengine/godot/files/10396445/transparency_bug.zip)

singleton = this;
}
SceneShaderForwardClustered::~SceneShaderForwardClustered() {
	RendererRD::MaterialStorage *material_storage = RendererRD::MaterialStorage::get_singleton();
	RD::get_singleton()->free(default_vec4_xform_buffer);
	RD::get_singleton()->free(shadow_sampler);
	material_storage->shader_free(overdraw_material_shader);
	material_storage->shader_free(default_shader);
	material_storage->material_free(overdraw_material);
	material_storage->material_free(default_material);
}
void SceneShaderForwardClustered::init(const String p_defines) {
	RendererRD::MaterialStorage *material_storage = RendererRD::MaterialStorage::get_singleton();
	{
		Vector<String> shader_versions;
		shader_versions.push_back("\n#define MODE_RENDER_DEPTH\n"); 
		shader_versions.push_back("\n#define MODE_RENDER_DEPTH\n#define MODE_DUAL_PARABOLOID\n"); 
		shader_versions.push_back("\n#define MODE_RENDER_DEPTH\n#define MODE_RENDER_NORMAL_ROUGHNESS\n"); 
		shader_versions.push_back("\n#define MODE_RENDER_DEPTH\n#define MODE_RENDER_NORMAL_ROUGHNESS\n#define MODE_RENDER_VOXEL_GI\n"); 
		shader_versions.push_back("\n#define MODE_RENDER_DEPTH\n#define MODE_RENDER_MATERIAL\n"); 
		shader_versions.push_back("\n#define MODE_RENDER_DEPTH\n#define MODE_RENDER_SDF\n"); 
		shader_versions.push_back("\n#define USE_MULTIVIEW\n#define MODE_RENDER_DEPTH\n"); 
		shader_versions.push_back("\n#define USE_MULTIVIEW\n#define MODE_RENDER_DEPTH\n#define MODE_RENDER_NORMAL_ROUGHNESS\n"); 
		shader_versions.push_back("\n#define USE_MULTIVIEW\n#define MODE_RENDER_DEPTH\n#define MODE_RENDER_NORMAL_ROUGHNESS\n#define MODE_RENDER_VOXEL_GI\n"); 
		Vector<String> color_pass_flags = {
			"\n#define MODE_SEPARATE_SPECULAR\n", 
			"\n#define USE_LIGHTMAP\n", 
			"\n#define USE_MULTIVIEW\n", 
			"\n#define MOTION_VECTORS\n",