I am suggesting your option 2, to be clearer. The other underground is a separate line, which is why i would not like it to underground at all.

it slows my game down to around 45 UPS but thats about it.

I would but i need to be holding shift and ctrl in order to angry ghost it...

Due to angry ghosting, screenshot hotkeys did not work, sorry :D

In the screenshot above, I was trying to angry ghost a rocket turret, but the smart belt system decided it should go under instead, when I was expecting it to just delete the normal belts and not try to tunnel under the turret ...