There's no such thing as pollution-free transportation. Even walking requires (in the modern world) clothes, shoes, and food produced on farms that use some kind of (even organic) fertilizer and diesel/gas-powered equipment, and that came to you on trucks (and maybe also trains in some parts of the country/world).

Electric (x) mode is remote-emission rather than local emission, which can be worthwhile in a number of ways. As the quote from PG&E notes, electricity can also be generated in a number of ways not all of which are major emitters of ghgs. California in general has a higher proportion of "clean" electricity sources than Back East or other places where coal is still used in quantity (though much less so even there than in years past), so electric-powered transportation is still generally cleaner overall than burning fuel in even the latest cleanest conventional vehicles and diesels.

That's not the main reason some commuter railroads want to go electric, though: the real reason is that to provide frequent service requires either very light vehicles (diesel LRVs) or electric due to the acceleration needed for that improved service. To go beyond basic commuter service, a line like Caltrain needs electric power for that reason. HSR needs electric power because it isn't practical for weight and fuel cost reasons to do diesel power for speeds over 125 mph (the British have documented that very well). So they need electric for operational reasons - any environmental benefit (there ARE benefits, both locally and globally, under California conditions) is useful but secondary to the decisions.