Hold on Rolin!
A couple of thongs.
To get a correct result for a hardpoint you need firstly have to have a element which covers the area of the model where the joint will be. Getting your calculator to do that would be a bit difficult, unless you can select which elements must be covered by the hardpoint.
Secondly, automatically deleting bulkheads is all well and good, but it gives you no way back. That is why, I leave them in until I'm 100% sure I'm finished, and then just manually delete the ones which are no longer needed. Once again, some bulkheads are needed as the stump of a torn off wing, or cockpit interior.

What would be great, as you mentioned, is an error report, showing where the RS goes wrong. we have a text dump of Gurney's RS calc, but the readout you get, although does help pin down the error, it's result leave most people completely lost.