OK. I’m missing something. But, home brewing is one of my hobbies and I just bottled and sampled a 14% mead so keep that in mind.
If you want/need the wire to go through the connector to something on the other side you might need just need to learn to make your own symbol. 
In this case just open the symbol in the editor, lose the graphics and set the pin length to zero. Put a box around it if you like and save it to a new library that won’t get over written on updates. It will end up looking like the footprint for header pins but will be more legible in this case I think.