Editing how bools appear in the Inspector

You could do this fairly easily with a custom editor, however if this was something that occurs in numerous scripts I would suggest putting all spaces into a single object and creating a custom PropertyDrawer, something along the lines of;

 [System.Serializable]
 public struct Spaces
 {
     public bool space1;
     public bool space2;
     public bool space3;
     public bool space4;
     public bool space5;
     public bool space6;
     public bool space7;
     public bool space8;
     public bool space9;
 }
 
 ...
 
 using UnityEditor;
 
 [CustomPropertyDrawer (typeof (Spaces))]
 public class SpacesDrawer : PropertyDrawer
 {
     public override void OnGUI (Rect a_Rect, SerializedProperty a_Property, GUIContent a_Label)
     {
         //Shorthand to make writing easier
         float lh = EditorGUIUtility.singleLineHeight;
 
         //Draw our label in the full rect (will self centre) but leave room at the end for the bools
         Rect labelRect = new Rect (a_Rect.x, a_Rect.y, a_Rect.width - lh * 3f, a_Rect.height);
         EditorGUI.LabelField (labelRect, a_Label);
 
         //This is where the bools will start on the x-axis
         float boolStartX = a_Rect.x + labelRect.width;
         //Initialise the bool rect to the top-left corner (1 line wide and tall)
         Rect boolRect = new Rect (boolStartX, a_Rect.y, lh, lh);
         //We want the bools to go left -> right then top -> bottom, so start with the y-axis as the outside loop
         for (int y = 0; y < 3; y++)
         {
             //Re-initialise the x-axis with every new row
             boolRect.x = boolStartX;
             for (int x = 0; x < 3; x++)
             {
                 //Find the current index (starting at 1)
                 int currentBool = x + y * 3 + 1;
                 //Draw the bool as normal (without a label)
                 EditorGUI.PropertyField (boolRect, a_Property.FindPropertyRelative ("space" + currentBool), GUIContent.none);
                 //Move to the next bool in the row
                 boolRect.x += boolRect.height;
             }
             //Move to the next row of bools
             boolRect.y += boolRect.width;
         }
     }
 
     //We need to override the property height - let's make it 3 lines (a regular property will be 1 line high)
     public override float GetPropertyHeight (SerializedProperty a_Property, GUIContent a_Label)
     {
         return EditorGUIUtility.singleLineHeight * 3f;
     }
 }