Three things to contribute:
Firstly, the third creature did not have a penis. It had a large tail that swept forward. I'm afraid I can't speak for the rest of you, but MY penis does not have a large sickle-shaped claw on the end of it just waiting to dice some poor prey to pieces. You are seeing what you want to see when you see a penis.
Secondly, I believe the second creature crashed because the creator -somehow- created pieces that were floating in midair. He attempted to delete one, but he missed another in his haste to go to the animation screen, and I believe that is why it crashed.
Finally, if you watch closely the pieces do resize, but only during an animation. This leads me to believe that instead of using the EXACT sizes and such of pieces, the editor uses approximations in the final product. I believe the game will ever-so-slightly modify your creature to make it more aesthetically pleasing, and also to make it easier to work in-game. I haven't said anything of this so far (but then again, I've only actually started talking on this forum recently), but evidence of this goes all the way back to the GDC '05 video. If you watch closely, the Willosaurus in-game has a much more rounded tail than the Willosaurus in the editor, whose tail was squashed and a bit kinked. Many other creatures have subtle changes between the editor and the game as well.