Ah, I see what you mean. If you are replacing the old chain with a new one, then you can push out any pin all the way to achieve your objective. However, if you intend to replace the chain you are removing, push out a non-special pin all the way. When you replace it, you will need to buy a new joining pin which has a guide section attached. You then press that pin in as far as is necessary to leave it the same height as the other pins. You then snap off the attached guide section (which should now be protruding from the far side of the chain) with pliers and free off the link as necessary.
The instructions in the link about not pushing the pin out the whole way do not apply to Shimano chains.