Sorry to say, but you need to home your axis so your printer knows where it is located in the physical world, you can establish your homing location in marlin and even set some safe homing position for Z but at the end you need to home all your axis.
Now usually the bolt you are talking about gets "covered" with a glass sheet (where you print).
But here is how to fix it easily:
On your start g code, before G28, do a G1 Z5 F1200, that will raise your z axis to prevent it from hitting the bolt, instead of G28 only, do a G28 X0 Y0, then move again your axis after the G28 and then do a G28 Z0.
If that's to complicated, raise your Z as before do a G28 but set a safe Z homing position in marlin.
Homing is required but you can tell the printer where to do it.
Edited 1 time(s). Last edit at 11/10/2014 08:44PM by ggherbaz.