### Godot version

4.1.1 stable

### System information

Windows 10

### Issue description

this is the default size loaded on startup 1024 which seems fine but it actually have loaded the default [2048] and ignored the size in project settings
![image](https://github.com/godotengine/godot/assets/53877170/c8c71de7-468a-487f-8e6c-dba1ce0f8fa5)

changing it now to any size will break it 
[2048]
![image](https://github.com/godotengine/godot/assets/53877170/3082ff09-b7d7-41f7-8fbb-813074a54135)

[512]
![image](https://github.com/godotengine/godot/assets/53877170/5ea4620f-52b5-4d0e-a5f5-747e777cd59d)


### Steps to reproduce

change 2d shadow atlas size in project settings while using compatibility renderer. 

### Minimal reproduction project

_
uint16_t *bone16w = (uint16_t *)&uptr[base_offset + i * stride];
				bone16w[0] = bone_ptr[i * 4 + 0];
				bone16w[1] = bone_ptr[i * 4 + 1];
				bone16w[2] = bone_ptr[i * 4 + 2];
				bone16w[3] = bone_ptr[i * 4 + 3];
			}
			base_offset += 2;
		} else {
			glDisableVertexAttribArray(RS::ARRAY_BONES);
		}
		if ((uint32_t)p_weights.size() == vertex_count * 4) {
			glEnableVertexAttribArray(RS::ARRAY_WEIGHTS);
			glVertexAttribPointer(RS::ARRAY_WEIGHTS, 4, GL_FLOAT, GL_FALSE, stride * sizeof(float), CAST_INT_TO_UCHAR_PTR(base_offset * sizeof(float)));
			const float *weight_ptr = p_weights.ptr();
			for (uint32_t i = 0; i < vertex_count; i++) {
				uint16_t *weight16w = (uint16_t *)&uptr[base_offset + i * stride];
				weight16w[0] = CLAMP(weight_ptr[i * 4 + 0] * 65535, 0, 65535);
				weight16w[1] = CLAMP(weight_ptr[i * 4 + 1] * 65535, 0, 65535);
				weight16w[2] = CLAMP(weight_ptr[i * 4 + 2] * 65535, 0, 65535);
				weight16w[3] = CLAMP(weight_ptr[i * 4 + 3] * 65535, 0, 65535);
			}
			base_offset += 2;
		} else {
			glDisableVertexAttribArray(RS::ARRAY_WEIGHTS);
		}
		ERR_FAIL_COND_V(base_offset != stride, 0);
		GLES3::Utilities::get_singleton()->buffer_allocate_data(GL_ARRAY_BUFFER, pb.vertex_buffer, vertex_count * stride * sizeof(float), polygon_buffer.ptr(), GL_STATIC_DRAW, "Polygon 2D vertex buffer");
	}
	if (p_indices.size()) {