diff --git a/editor/animation/animation_track_editor.cpp b/editor/animation/animation_track_editor.cpp
index 7e5b909725f..b20108abde4 100644
--- a/editor/animation/animation_track_editor.cpp
+++ b/editor/animation/animation_track_editor.cpp
@@ -1897,7 +1897,7 @@ void AnimationTimelineEdit::_play_position_draw() {
 	}
 
 	float scale = get_zoom_scale();
-	int h = play_position->get_size().height;
+	int h = editor->box_selection_container->get_global_position().y - get_global_position().y;
 
 	int px = (-get_value() + play_position_pos) * scale + get_name_limit();
 
@@ -5550,7 +5550,11 @@ void AnimationTrackEditor::_notification(int p_what) {
 			imported_anim_warning->set_button_icon(get_editor_theme_icon(SNAME("NodeWarning")));
 			dummy_player_warning->set_button_icon(get_editor_theme_icon(SNAME("NodeWarning")));
 			inactive_player_warning->set_button_icon(get_editor_theme_icon(SNAME("NodeWarning")));
-			main_panel->add_theme_style_override(SceneStringName(panel), get_theme_stylebox(SceneStringName(panel), SNAME("Tree")));
+
+			Ref<StyleBox> panel_style = get_theme_stylebox(SceneStringName(panel), SNAME("Tree"))->duplicate();
+			panel_style->set_content_margin(SIDE_TOP, get_theme_constant("base_margin", EditorStringName(Editor)) * EDSCALE);
+			main_panel->add_theme_style_override(SceneStringName(panel), panel_style);
+
 			edit->get_popup()->set_item_icon(edit->get_popup()->get_item_index(EDIT_ADD_RESET_KEY), get_editor_theme_icon(SNAME("MoveUp")));
 			edit->get_popup()->set_item_icon(edit->get_popup()->get_item_index(EDIT_APPLY_RESET), get_editor_theme_icon(SNAME("Reload")));
 			auto_fit->set_button_icon(get_editor_theme_icon(SNAME("AnimationAutoFit")));
diff --git a/editor/themes/theme_modern.cpp b/editor/themes/theme_modern.cpp
index 1517b7ed586..2ba77e1a024 100644
--- a/editor/themes/theme_modern.cpp
+++ b/editor/themes/theme_modern.cpp
@@ -2382,7 +2382,7 @@ void ThemeModern::populate_editor_styles(const Ref<EditorTheme> &p_theme, Editor
 	{
 		// Timeline general.
 
-		p_theme->set_constant("timeline_v_separation", "AnimationTrackEditor", 0);
+		p_theme->set_constant("timeline_v_separation", "AnimationTrackEditor", p_config.base_margin * EDSCALE);
 		p_theme->set_constant("track_v_separation", "AnimationTrackEditor", 0);
 
 		int margin = p_theme->get_stylebox(SceneStringName(panel), SNAME("PanelContainer"))->get_content_margin(SIDE_LEFT);