### Godot version

v4.0.beta14.official [28a24639c]

### System information

Windows 10, OpenGL

### Issue description

Vulkan and Mobile:
![Godot_v4 0-beta14_win64_kEcRNiMfNJ](https://user-images.githubusercontent.com/7782218/213967627-8e8755d9-2fe2-43b3-b197-f9f2840b7580.gif)

OpenGL:
![Godot_v4 0-beta14_win64_MQ233TZuPq](https://user-images.githubusercontent.com/7782218/213967651-ae463a6f-c867-4312-bdf1-525e1d7def01.gif)

At first I thought it was related to `set_buffer()`, but it turned out that `set_instance_*` also work incorrectly.
Probably the custom information is also set incorrectly, but I haven't checked it yet.

### Steps to reproduce

* Open MRP
* In the editor, select `MeshInstance3D` node and change the `Count` property
* -- or --
* Start the project and move the slider

You can also switch the renderer to Vulkan and compare.

### Minimal reproduction project

[set_buffer().zip](https://github.com/godotengine/godot/files/10476834/set_buffer.zip)

if (!array_is_2d) {
					if ((mi->surfaces[i].format_cache & (1 << RS::ARRAY_NORMAL))) {
						specialization |= SkeletonShaderGLES3::USE_NORMAL;
					}
					if ((mi->surfaces[i].format_cache & (1 << RS::ARRAY_TANGENT))) {
						specialization |= SkeletonShaderGLES3::USE_TANGENT;
					}
				}
				bool success = skeleton_shader.shader.version_bind_shader(skeleton_shader.shader_version, variant, specialization);
				if (!success) {
					continue;
				}
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::BLEND_WEIGHT, base_weight, skeleton_shader.shader_version, variant, specialization);
				skeleton_shader.shader.version_set_uniform(SkeletonShaderGLES3::BLEND_SHAPE_COUNT, float(mi->mesh->blend_shape_count), skeleton_shader.shader_version, variant, specialization);
				glBindBuffer(GL_ARRAY_BUFFER, 0);
				glBindVertexArray(mi->mesh->surfaces[i]->skeleton_vertex_array);
				glBindBufferBase(GL_TRANSFORM_FEEDBACK_BUFFER, 0, mi->surfaces[i].vertex_buffers[0]);
				glBeginTransformFeedback(GL_POINTS);
				glDrawArrays(GL_POINTS, 0, mi->mesh->surfaces[i]->vertex_count);
				glEndTransformFeedback();
				variant = SkeletonShaderGLES3::MODE_BLEND_PASS;
				success = skeleton_shader.shader.version_bind_shader(skeleton_shader.shader_version, variant, specialization);
				if (!success) {
					continue;
				}
				
				for (uint32_t bs = 0; bs < mi->mesh->blend_shape_count - 1; bs++) {
					float weight = mi->blend_weights[bs];
					if (Math::is_zero_approx(weight)) {