I was surprised to read that the cost of the underpass had risen to $33 million but accept the arguments that strengthening for the overpass loading and the complex diversions required to achieve that would escalate costs significantly.
However, it seems that other options haven't been seriously considered so how about this: rather than have one single underpass have two under each northern on/off ramp.
This could be constructed after the main straight-through overpass/bridge has been completed and is operational thereby minimising diversion requirements. It could possibly utilise each end of the existing underpass.
The compromise is that