Hey John, the Nelson Bennett tunnel is still double track, at least at the PSMRE ( www.psmre.org ). Seriously, it was originally double track and yep the Double Stacks and Autorack forced it to single track. Others more knowledgeable than I, have said the cost to double track it again would be prohibitive.

BNSF does indeed to a good job of keeping it available for the Passenger trains. Frequently I hear trains being told they'll have to wait for an Amtrak, and it is often a suprising (for me anyway) distance away. Short of something gone wrong, I never hear Amtrak being told they will have to wait to run through the tunnels.