How to export .OBJ from Editor with rescaled mesh?

Here is an editor script that should do the job for you. It takes an object and makes a clone that has local scale of (1,1,1) and rotation (0,0,0). Place the script in the 'Assets/Editor' folder. It must be named 'RotateMesh'. To use select the object in the hierarchy, and select 'RotateMesh' from the 'Window' menu. It is only lightly tested at this point.

 using UnityEngine;
 using UnityEditor;
 using System.Collections.Generic;
 
 public class RotateMesh : EditorWindow {
     
     private string error = "";
     
     [MenuItem("Window/Rotate Mesh %#r")]
     public static void ShowWindow() {
         EditorWindow.GetWindow(typeof(RotateMesh));
     }
 
     void OnGUI() {
         Transform curr = Selection.activeTransform;
         GUILayout.Label ("Creates a clone of the game object with a rotated mesh\n" + 
             "so that the rotation will be (0,0,0) and the scale will\nbe (1,1,1).");
         GUILayout.Space(20);
 
         if (GUILayout.Button ("Rotate Mesh")) {
             error = "";
             RotateTheMesh();
         }
         
         GUILayout.Space(20);
         GUILayout.Label(error);
     }
     
     void RotateTheMesh() {
         List<Transform> children = new List<Transform>();
         Transform curr = Selection.activeTransform;
 
         MeshFilter mf;
         if (curr == null) {
             error = "No appropriate object selected.";
             Debug.Log (error);    
             return;
         }
         
         if (curr.localScale.x < 0.0 || curr.localScale.y < 0.0f || curr.localScale.z < 0.0f) {
             error = "Cannot process game objecrt with negative scale values.";
             Debug.Log (error);
             return;
         }
         
         mf = curr.GetComponent<MeshFilter>();
         if (mf == null || mf.sharedMesh == null) {
             error = "No mesh on the selected object";
             Debug.Log (error);
             return;
         }
         
         // Create the duplicate game object
         GameObject go = Instantiate (curr.gameObject) as GameObject;
         mf = go.GetComponent<MeshFilter>();
         mf.sharedMesh = Instantiate (mf.sharedMesh) as Mesh;
         curr = go.transform;
         
         // Disconnect any child objects and same them for later
         foreach (Transform child in curr) {
             if (child != curr) {
                 children.Add (child);
                 child.parent = null;
             }
         }
         
         // Rotate and scale the mesh
         Vector3[] vertices = mf.sharedMesh.vertices;
         for (int i = 0; i < vertices.Length; i++) {
             vertices[i] = curr.TransformPoint(vertices[i]) - curr.position;
         }
         mf.sharedMesh.vertices = vertices;
 
         
         // Fix the normals
         Vector3[] normals = mf.sharedMesh.normals;
         if (normals != null) {
             for (int i = 0; i < normals.Length; i++)
                 normals[i] = curr.rotation * normals[i];
         }
         mf.sharedMesh.normals = normals;
         mf.sharedMesh.RecalculateBounds();
         
         curr.transform.rotation = Quaternion.identity;
         curr.localScale = new Vector3(1,1,1);
     
         // Restore the children
         foreach (Transform child in children) {
             child.parent = curr;
         }
         
         // Set selection to new game object
         Selection.activeObject = curr.gameObject;
 
         //--- Do a rudamentary fixup of mesh, box, and sphere colliders----
         MeshCollider mc = curr.GetComponent<MeshCollider>();
         if (mc != null) {
             mc.sharedMesh = mf.sharedMesh;
         }
         
         BoxCollider bc = curr.GetComponent<BoxCollider>();
         if (bc != null) {
             DestroyImmediate(bc);
             curr.gameObject.AddComponent<BoxCollider>();
         }
         SphereCollider sc = curr.GetComponent<SphereCollider>();
         if (sc != null) {
             DestroyImmediate(sc);
             curr.gameObject.AddComponent<SphereCollider>();
         }
         
         if (curr.GetComponent<Collider>()) {
             error = "Be sure to verify size of collider.";
         }
         
         // Save a copy to disk
         string name = "Assets/Editor/"+go.name+Random.Range (0, int.MaxValue).ToString()+".asset";
         AssetDatabase.CreateAsset(mf.sharedMesh, name);
         AssetDatabase.SaveAssets();
     }
 }