Should I be scared because there's no leaves at 12'' above the graft?
Yes, I believe so. I would suggest waiting on the pugging until your tree has been established in its new home to minimize stress. I successfully pugged two mango trees below the leaves, but my trees are in-ground and in sunny south Florida. I can also get replacement grafted mango trees locally for $25 in case I kill them, which I think you cannot. Pugging the tree will stress your tree. Please make sure your tree has PLENTY of water, don't drown it, but make sure it is properly hydrated. Look at the leaves and see the "bud" at the base of the leaf. Look for these buds on your tree's trunk, make sure you cut above an area that has a few of these buds to encourage new branch growth from the buds. Ensure your cut is "clean" to aid in healing, rather than a jagged sloppy cut.
Haden is a large tree. In your future acquisitions, perhaps get a tree that naturally dwarfs, such as Pickering or Cogshall. I just pugged a Harvest Moon below the leaves. I have no experience with indoor growing.
Trees get that lolly pop shape because they are grown in large nurseries next to eachother and have to grow upward to get light.
