If you owner build, without the right permits, and then tried to refinance, the bank may find out, as suddenly having a house on what they thought was a vacant block might make the assessor ask questions. If you went to a second bank, it might be ok, but why go to the trouble of owner building without the right permits? The cost diferential cant be that much? As to selling the property, the next owner after a period of time might not be liable for you not having a permit, but that wouldnt necessarily mean you are not still held liable.
Why not just build a kit home, or OB with the right permits? Why not get plans for a house approved and see what that does to the valuation and LVR?