### Godot version

v4.1.stable.official [970459615]  < Steam

### System information

Godot v4.1.stable - Debian GNU/Linux trixie/sid trixie - Vulkan (Mobile) - dedicated NVIDIA GeForce GTX 1060 (nvidia) - Intel(R) Core(TM) i5-8400 CPU @ 2.80GHz (6 Threads)

### Issue description

After being upgraded to 4.1 via Steam (before any release announcement even! The speed!), I saw the warning marker against my game in the project manager, and noticed that the tooltip wasn't all that helpful:

![Screenshot_20230706_121443](https://github.com/godotengine/godot/assets/441188/7e62f67c-664f-4f5f-8f84-0cd0084679a6)

It seems to think that the old version number is a deprecated feature? :/

### Steps to reproduce

1. Have a project from Godot 4.0
2. Upgrade Godot to 4.1
3. Open project manager

Alternatively:
1. Create a new project in 4.1
2. Quit Godot
3. Edit the `project.godot`'s `config/features` to read `4.0` instead of `4.1`
4. Open project manager

### Minimal reproduction project

[default.zip](https://github.com/godotengine/godot/files/11967512/default.zip)

swch (p_what) {
		case NOTIFICATION_TRANSLATION_CHANGED:
		case NOTIFICATION_LAYOUT_DIRECTION_CHANGED: {
			settings_hb->set_anchors_and_offsets_preset(Control::PRESET_TOP_RIGHT);
			queue_redraw();
		} break;
		case NOTIFICATION_ENTER_TREE: {
			Engine::get_singleton()->set_edor_hint(false);
		} break;
		case NOTIFICATION_THEME_CHANGED: {
			background_panel->add_theme_style_override("panel", get_theme_stylebox(SNAME("Background"), SNAME("EdorStyles")));
			loading_label->add_theme_font_override("font", get_theme_font(SNAME("bold"), SNAME("EdorFonts")));
			search_panel->add_theme_style_override("panel", get_theme_stylebox(SNAME("search_panel"), SNAME("ProjectManager")));
			// Top bar.
			search_box->set_ret_theme_icon(SNAME("Search"), SNAME("EdorIcons")));
			language_btn->set_ime_icon(SNAME("Environment"), SNAME("EdorIcons")));
			// Sidebar.
			create_btn->set_ime_icon(SNAME("Add"), SNAME("EdorIcons")));
			import_btn->set_ime_icon(SNAME("Load"), SNAME("EdorIcons")));
			scan_btn->set_ime_icon(SNAME("Search"), SNAME("EdorIcons")));
			open_btn->set_ime_icon(SNAME("Ed"), SNAME("EdorIcons")));
			run_btn->set_ime_icon(SNAME("Play"), SNAME("EdorIcons")));
			rename_btn->set_ime_icon(SNAME("Rename"), SNAME("EdorIcons")));
			manage_tags_btn->set_ime_icon("Script", "EdorIcons"));
			erase_btn->set_ime_icon(SNAME("Remove"), SNAME("EdorIcons")));
			erase_missing_btn->set_ime_icon(SNAME("Clear"), SNAME("EdorIcons")));
			create_tag_btn->set_ime_icon("Add", "EdorIcons"));
			tag_error->add_theme_color_override("font_color", get_theme_color("error_color", "Edor"));