### 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)

uses_discard = false;
	uses_roughness = false;
	uses_normal = false;
	bool wireframe = false;
	unshaded = false;
	uses_vertex = false;
	uses_position = false;
	uses_sss = false;
	uses_transmittance = false;
	uses_screen_texture = false;
	uses_depth_texture = false;
	uses_normal_texture = false;
	uses_time = false;
	writes_modelview_or_projection = false;
	uses_world_coordinates = false;
	uses_particle_trails = false;
	int depth_drawi = DEPTH_DRAW_OPAQUE;
	ShaderCompiler::IdentifierActions actions;
	actions.entry_point_stages["vertex"] = ShaderCompiler::STAGE_VERTEX;
	actions.entry_point_stages["fragment"] = ShaderCompiler::STAGE_FRAGMENT;
	actions.entry_point_stages["light"] = ShaderCompiler::STAGE_FRAGMENT;
	actions.render_mode_values["blend_add"] = Pair<int *, int>(&blend_mode, BLEND_MODE_ADD);
	actions.render_mode_values["blend_mix"] = Pair<int *, int>(&blend_mode, BLEND_MODE_MIX);
	actions.render_mode_values["blend_sub"] = Pair<int *, int>(&blend_mode, BLEND_MODE_SUB);
	actions.render_mode_values["blend_mul"] = Pair<int *, int>(&blend_mode, BLEND_MODE_MUL);
	actions.render_mode_values["alpha_to_coverage"] = Pair<int *, int>(&alpha_antialiasing_mode, ALPHA_ANTIALIASING_ALPHA_TO_COVERAGE);
	actions.render_mode_values["alpha_to_coverage_and_one"] = Pair<int *, int>(&alpha_antialiasing_mode, ALPHA_ANTIALIASING_ALPHA_TO_COVERAGE_AND_TO_ONE);
	actions.render_mode_values["depth_draw_never"] = Pair<int *, int>(&depth_drawi, DEPTH_DRAW_DISABLED);
	actions.render_mode_values["depth_draw_opaque"] = Pair<int *, int>(&depth_drawi, DEPTH_DRAW_OPAQUE);
	actions.render_mode_values["depth_draw_always"] = Pair<int *, int>(&depth_drawi, DEPTH_DRAW_ALWAYS);