### 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)

actions.usage_defines["NORMAL_MAP"] = "#define NORMAL_MAP_USED\n";
		actions.usage_defines["NORMAL_MAP_DEPTH"] = "@NORMAL_MAP";
		actions.usage_defines["COLOR"] = "#define COLOR_USED\n";
		actions.usage_defines["INSTANCE_CUSTOM"] = "#define ENABLE_INSTANCE_CUSTOM\n";
		actions.usage_defines["POSITION"] = "#define OVERRIDE_POSITION\n";
		actions.usage_defines["ALPHA_SCISSOR_THRESHOLD"] = "#define ALPHA_SCISSOR_USED\n";
		actions.usage_defines["ALPHA_HASH_SCALE"] = "#define ALPHA_HASH_USED\n";
		actions.usage_defines["ALPHA_ANTIALIASING_EDGE"] = "#define ALPHA_ANTIALIASING_EDGE_USED\n";
		actions.usage_defines["ALPHA_TEXTURE_COORDINATE"] = "@ALPHA_ANTIALIASING_EDGE";
		actions.usage_defines["SSS_STRENGTH"] = "#define ENABLE_SSS\n";
		actions.usage_defines["SSS_TRANSMITTANCE_DEPTH"] = "#define ENABLE_TRANSMITTANCE\n";
		actions.usage_defines["BACKLIGHT"] = "#define LIGHT_BACKLIGHT_USED\n";
		actions.usage_defines["SCREEN_TEXTURE"] = "#define SCREEN_TEXTURE_USED\n";
		actions.usage_defines["SCREEN_UV"] = "#define SCREEN_UV_USED\n";
		actions.usage_defines["DIFFUSE_LIGHT"] = "#define USE_LIGHT_SHADER_CODE\n";
		actions.usage_defines["SPECULAR_LIGHT"] = "#define USE_LIGHT_SHADER_CODE\n";
		actions.usage_defines["FOG"] = "#define CUSTOM_FOG_USED\n";
		actions.usage_defines["RADIANCE"] = "#define CUSTOM_RADIANCE_USED\n";
		actions.usage_defines["IRRADIANCE"] = "#define CUSTOM_IRRADIANCE_USED\n";
		actions.usage_defines["MODEL_MATRIX"] = "#define MODEL_MATRIX_USED\n";
		actions.render_mode_defines["skip_vertex_transform"] = "#define SKIP_TRANSFORM_USED\n";
		actions.render_mode_defines["world_vertex_coords"] = "#define VERTEX_WORLD_COORDS_USED\n";
		actions.render_mode_defines["ensure_correct_normals"] = "#define ENSURE_CORRECT_NORMALS\n";
		actions.render_mode_defines["cull_front"] = "#define DO_SIDE_CHECK\n";
		actions.render_mode_defines["cull_disabled"] = "#define DO_SIDE_CHECK\n";
		actions.render_mode_defines["particle_trails"] = "#define USE_PARTICLE_TRAILS\n";
		actions.render_mode_defines["depth_draw_opaque"] = "#define USE_OPAQUE_PREPASS\n";
		bool force_lambert = GLOBAL_GET("rendering/shading/overrides/force_lambert_over_burley");
		if (!force_lambert) {
			actions.render_mode_defines["diffuse_burley"] = "#define DIFFUSE_BURLEY\n";