I found it is possible to export flip info in bone setup mode.

...
   "bones":[
      {
         "name":"root",
         "scaleX":0.562,
         "scaleY":0.562,
         "flipX":true,                 // like this example line
         "color":"5bff00ff"
      },
...

But in SkeletonJson.c,function "spSkeletonJson_readSkeletonData",line 468,the bone data initialization logic,I think the flip setting is missed.(At least in official runtime repo revision 20141018,SHA1:df792f3d)
I added following lines,and my problem solved:

boneData->flipX = Json_getInt(boneMap, "flipX", 0);
boneData->flipY = Json_getInt(boneMap, "flipY", 0);

BTW:I think there is another missing line in Json.c,function "parse_value",line 272.
The "item->type = Json_False;" is ok.But seems missing "item->valueInt = 0;" there compare to the logic of case 't'.
Although the initialization of item->valueInt is 0.The missing line caused the purpose being a bit unclear....