Fuller details of a somewhat different tunnel can be found in the Bureau of Transport and Regional Economics Working Paper 53 (2002), at http://www.btre.gov.au/docs/wp_53/index.html.
The BTRE paper:

• discusses premium tolls (higher than $3.50) at peak hours (see the Executive Summary).
• has no answer for where the exhaust emissions are to be discharged
• costs the underwater part of the tunnel at only $190 million. Given that it is far longer than the Harbour Tunnel, we are entitled to wonder what the actual cost might be
• points out that significant growth in traffic on the Warringah peninsula would take away some of the area's unique character, making it just another Sydney suburb.

• Even though the political leaflet suggests that the existing surface route would remain available, it is certain that pressure would be exerted by the tunnel operators to restrict its capacity. This would probably result in kerbside lane parking being restored around Spit Junction, and possibly in a lane of Spit Hill being removed for the construction of a safety fence. The extra capacity of the new tunnel would not be achieved.
• It is certain that expanding the capacity of a congested route like The Spit would be followed by an increase in traffic volumes. The extra traffic would exacerbate congestion elsewhere, e.g. on the Harbour Bridge. Travel time savings claimed for the new tunnel would be offset by delays elsewhere.
• Similarly, air pollution would be worse once the new tunnel was operating and traffic volumes had grown.
• There are both State and Federal policies to limit the current surge in private car use; constructing the tunnel would contravene those policies. Ironically, the same web site also has discussion of growth in car travel - see report "Greenhouse Gas Emissions from Transport - Australian Trends to 2020" on http://www.btre.gov.au//docs/r107/index.html.