I think the case for using hydrogen today is pretty weak, but a lot of the details for why it's a bad choice are (as you say) exacerbated by the one-off deploys of the technology. If you were testing gas busses and needed to truck gasoline in just for your busses you would expect the numbers to get worse too.

My view is that if you want a clean alternative today you'd go with electric and also the tech seems worth continuing to develop for other applications. I also think that public transit doesn't seem like it plays to the strengths (such as they are) of hydrogen.