The Pioneer Institute is absolutely arguing in bad faith, but there are legitimate points made. And while too much focus on cost control will lead to neglecting service quality, too little means that far less service is provided than could be with those funds. In particular, the increases in bus operating costs (64% revenue miles) from 2019 to 2023 are nothing to sneeze at. It's hard to say exactly what caused that, and the NTD numbers for 2024 should be interesting. However, Pioneer shows their hand by providing data on revenue hours (increase of 94% over the same time period), which is almost certainly a worse metric.
While this is clearly hypocritical, it is fair to ask why MSP and the T need their own pensions instead of just integrating into the state's. Larger pension funds are, in general, able to achieve higher rates of return all else being equal. There is also the benefit of pension costs not being a drag on any specific agency and it being much harder to not fully fund those pensions. Ultimately, the pensions are almost certainly a result of the T and police having better unions than most state employees, which while good for them, is a pretty terrible reason for their pensions to be that much more generous.