Anything that can help make safer/more comfortable cycle routing is great step forward. Cycle routing is definitely more complex that driving because of the issue the article mentions.
I tried this out. My city is pretty notorious for having incomplete cycling infrastructure. i.e.) you get local areas that have cycle routes, but you often have to brave some craziness to get anywhere for real.
For my most common routes, it seems to be making the same choices as Google Maps. They definitely aren't the most optimal or comfortable choices, though I suspect this is at least partially a data problem. Steep grades, stairs, and difficult to find turns (more my city's fault that anything) are on the route, and it takes you though the straightforward but less safe connectors instead of detouring through neighbourhoods.
Perhaps one more tuning parameter is needed that would allow weighting stress vs distance?