Of course. You always need to model the outcomes and model what will get the best return on investment. The other is to model any other externalities as well.
For example bypasses will not impact traffic travelling into and out of a city where the point of origin or destination is that city. Where as people travelling by train will. The flip side is that the trainstations themselves will generate traffic wherever they are located so that needs to be planned for and handled as well.
Other considerations are pollution and noise. The HSR is likely to be noisier where it runs but for a relatively short period of time. Vehicles are individually quieter but in sum much louder, they are also more distributed. So you are trading a more general reduction in noise for greater noise levels at specific points for shorter durations.
As for pollution HSR will generate significantly less pollution per passenger mile but also move the pollution away from the population centre to the power generator.
Finally what is the long term maintenance costs? Road wears and wears fast as far as infrastructure goes. Rail on the other hand has a very long life cycle in comparison. Over what period of time would the capital and maintenance costs of bypasses exceed the capital and maintenance costs of the rail?
All of these things need to be taken into consideration when deciding if something is a viable plan. You can't just say - it cost $20 billion so it needs to be $100 per ticket to break even.