I, err... *coughs*... I mean... Yeah - it's... errm... 'different' alright.
What kind of shape are you that the saddle is that low, but you feel that you need such a monster stem?
You could still try removing the old wedge by putting the old stem in, and then trying to 'grab' the threads with the bolt, then screwing it in a few turns and then pulling it out.
Does the old stem still insert to the proper length OK I wonder? It shouldn't do really if for all intents and purposes it's identical to the new one, just longer. Hmm...
PS - I would have thought that internal rusting would have caused some scuffs and/or rust marks on the new stem after it's been inserted...